multiqc_data/llms-full.txt - Workdir - NFCORE_SAREK:SAREK:MULTIQC

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Filename: multiqc_data/llms-full.txt
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/e5f9e499e2398646b31d9e6edf05fc/multiqc_data/llms-full.txt
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Task: NFCORE_SAREK:SAREK:MULTIQC
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Content

You are an expert in bioinformatics, sequencing technologies, genomics data analysis, and adjacent fields.

You are given findings from a MultiQC report, generated by a bioinformatics workflow.
MultiQC supports various bioinformatics tools that output QC metrics, and aggregates those metrics
into a single report. It outputs a "General Statistics" table with key metrics for each sample across
all tools. That table is followed by more detailed sections from specific tools, that can include tables,
as well as plots of different types (bar plot, line plot, scatter plot, heatmap, etc.)

You are given data from such a report. Your task is to analyse the data, and
give 1-2 bullet points of a very short and concise overall summary for the results.
Don't waste words: mention only the important QC issues. If there are no issues, just say so.
Just print one or two bullet points, nothing else.
Please do not add any extra headers to the response.

Use markdown to format your reponse for readability. Use directives with pre-defined classes
.text-green, .text-red, and .text-yellow to highlight severity, e.g. :span[39.2%]{.text-red}.
Highlight any mentioned sample names or sample named prefixes or suffixes with a sample directive,
and make sure to use the same color classes for severity, e.g. :sample[A1001.2003]{.text-yellow}
or :sample[A1001]{.text-yellow}. Do not put multiple sample names inside one directive.

You must use only multiples of 4 spaces to indent nested lists.



Two examples of short summaries:

- :span[11/13 samples]{.text-green} show consistent metrics within expected ranges.
- :sample[A1001.2003]{.text-red} and :sample[A1001.2004]{.text-red} exhibit extremely high percentage of :span[duplicates]{.text-red} (:span[65.54%]{.text-red} and :span[83.14%]{.text-red}, respectively).

- All samples show good quality metrics with :span[75.7-77.0%]{.text-green} CpG methylation and :span[76.3-86.0%]{.text-green} alignment rates
- :sample[2wk]{.text-yellow} samples show slightly higher duplication (:span[11-15%]{.text-yellow}) compared to :sample[1wk]{.text-green} samples (:span[6-9%]{.text-green})'



----------------------

Tools used in the report:

1. altera/sarek Workflow Summary
Description: <ul>
<li>this information is collected when the pipeline is started.</li>
</ul>
Links: https://github.com/altera/sarek

----------------------

2. Samtools Flagstat
Description: <p>Toolkit for interacting with BAM/CRAM files.</p>
Links: http://www.htslib.org

----------------------

3. Mosdepth
Description: <p>Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.</p>
Links: https://github.com/brentp/mosdepth

----------------------

4. Bcftools
Description: <p>Utilities for variant calling and manipulating VCFs and BCFs.</p>
Links: https://samtools.github.io/bcftools/

----------------------

5. Vcftools
Description: <p>Program to analyse and reporting on VCF files.</p>
Links: https://vcftools.github.io

----------------------

6. SNPeff
Description: <p>Annotates and predicts the effects of variants on genes (such as amino acid changes).</p>
Links: http://snpeff.sourceforge.net/

----------------------

7. VEP
Description: <p>Determines the effect of variants on genes, transcripts and protein sequences, as well as regulatory regions.</p>
Links: https://www.ensembl.org/info/docs/tools/vep/index.html

----------------------

8. nf-core/sarek Methods Description
Description: <p>Suggested text and references to use when describing pipeline usage within the methods section of a publication.</p>
Links: https://github.com/nf-core/sarek

----------------------

----------------------

Tool: altera/sarek Workflow Summary
Section: 
<p style="font-size:110%"><b>Input/output options</b></p>
<dl class="dl-horizontal">
    <dt>input</dt><dd><samp>s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/samplesheet/workorder.csv</samp></dd>
    <dt>outdir</dt><dd><samp>s3://natera-rnd-pltf-dev-s3-gitlab-results/sarek/build2797494/baseline-run/63551853</samp></dd>
</dl>
<p style="font-size:110%"><b>Main options</b></p>
<dl class="dl-horizontal">
    <dt>hrd_coverage_profile</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/AIH/hrd_score_altera_bam/dbsnp_baseline_altera.260120.tsv.gz</samp></dd>
    <dt>intervals_dir</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals</samp></dd>
    <dt>intervals_vc_dir</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_padded_intervals</samp></dd>
    <dt>mimsi_microsatellites_list</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/mimsi/1500_dropped_panel_with_boosted_msi_regions.tsv</samp></dd>
    <dt>mimsi_model</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/mimsi/mi_msi_v0_4_0_200x_attn.model</samp></dd>
    <dt>tools</dt><dd><samp>ngscheckmate,contamination,tnseq,strelka,manta,msisensor2,mimsi,cnvkit,facets,tmb,hrd,whatshap,snpeff,merge,sentieon_haplotyper_rf,chip_detection,snv_indel,germline_cnv,sex_estimation</samp></dd>
    <dt>wes</dt><dd><samp>true</samp></dd>
</dl>
<p style="font-size:110%"><b>Variant Calling</b></p>
<dl class="dl-horizontal">
    <dt>chip_cohort_blacklist</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cohort_blacklist.bed.gz</samp></dd>
    <dt>chip_cosmic_heme</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cosmic_heme.tsv.gz</samp></dd>
    <dt>chip_encode_blacklist</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/encode_blacklist.bed.gz</samp></dd>
    <dt>chip_gene_family_blacklist</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_family_blacklist.bed.gz</samp></dd>
    <dt>chip_gene_tiers</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_tiers.tsv</samp></dd>
    <dt>chip_pon</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP_PON/pon.hotspot_protected.raw.vcf.gz</samp></dd>
    <dt>chip_pon_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP_PON/pon.hotspot_protected.raw.vcf.gz.tbi</samp></dd>
    <dt>cnvkit_reference</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/cnvkit/cnvkit_wes_altera.reference.cnn</samp></dd>
    <dt>pon</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz</samp></dd>
    <dt>pon_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz.tbi</samp></dd>
    <dt>pot</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/POT/aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz</samp></dd>
    <dt>pot_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/POT/aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz.tbi</samp></dd>
</dl>
<p style="font-size:110%"><b>General reference genome options</b></p>
<dl class="dl-horizontal">
    <dt>igenomes_base</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/</samp></dd>
    <dt>optitype_reference</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/optitype/original_v3.15_2014/</samp></dd>
</dl>
<p style="font-size:110%"><b>Reference genome options</b></p>
<dl class="dl-horizontal">
    <dt>blacklist_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/blacklist_grch38.bed.gz</samp></dd>
    <dt>blacklist_bed_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/blacklist_grch38.bed.gz.tbi</samp></dd>
    <dt>blacklist_header</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/blacklist_header.txt</samp></dd>
    <dt>conpair_markers</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Conpair/GRCh38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.liftover.bed</samp></dd>
    <dt>container_registry_seqera</dt><dd><samp>292967571998.dkr.ecr.us-west-2.amazonaws.com/community.wave.seqera.io</samp></dd>
    <dt>dbsnp</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz</samp></dd>
    <dt>dbsnp_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi</samp></dd>
    <dt>dbsnp_vqsr</dt><dd><samp>--resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz</samp></dd>
    <dt>dict</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict</samp></dd>
    <dt>exome_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/bed/xgen-exome-hyb-panel-v2-targets-hg38_short.mrg_chr21.bed</samp></dd>
    <dt>fasta</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta</samp></dd>
    <dt>fasta_fai</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai</samp></dd>
    <dt>genome_annotations</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ensembl/Homo_sapiens.GRCh38.110.gtf.gz</samp></dd>
    <dt>germline_rescue_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/germline_rescue_targets.bed</samp></dd>
    <dt>germline_resource</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz</samp></dd>
    <dt>germline_resource_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi</samp></dd>
    <dt>gt_correction_model</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/gt_correction_model_v2.joblib</samp></dd>
    <dt>gt_correction_threshold_grch38</dt><dd><samp>0.5</samp></dd>
    <dt>lowdepth_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_grch38.tsv.gz</samp></dd>
    <dt>lowdepth_bed_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_grch38.tsv.gz.tbi</samp></dd>
    <dt>lowdepth_header</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_header.txt</samp></dd>
    <dt>ngscheckmate_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed</samp></dd>
    <dt>probe_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/bed/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_chr21.bed</samp></dd>
    <dt>repeatmasker_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_grch38.bed.gz</samp></dd>
    <dt>repeatmasker_bed_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_grch38.bed.gz.tbi</samp></dd>
    <dt>repeatmasker_header</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_header.txt</samp></dd>
    <dt>rf_blacklist_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_blacklist.bed.gz</samp></dd>
    <dt>rf_blacklist_bed_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_blacklist.bed.gz.tbi</samp></dd>
    <dt>rf_boosted_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_boosted_exons.bed.gz</samp></dd>
    <dt>rf_boosted_bed_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_boosted_exons.bed.gz.tbi</samp></dd>
    <dt>rf_indel_fp_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_fp_regions.bed.gz</samp></dd>
    <dt>rf_indel_fp_bed_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_fp_regions.bed.gz.tbi</samp></dd>
    <dt>rf_indel_fp_rates_tsv</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_locus_fp_rates.tsv</samp></dd>
    <dt>rf_indel_model</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_rf_model_v7.joblib</samp></dd>
    <dt>rf_low_depth_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_low_depth.bed.gz</samp></dd>
    <dt>rf_low_depth_bed_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_low_depth.bed.gz.tbi</samp></dd>
    <dt>rf_repeatmasker_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz</samp></dd>
    <dt>rf_repeatmasker_bed_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz.tbi</samp></dd>
    <dt>rf_snv_fp_bed</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_fp_regions.bed.gz</samp></dd>
    <dt>rf_snv_fp_bed_tbi</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_fp_regions.bed.gz.tbi</samp></dd>
    <dt>rf_snv_model</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_rf_model_v4.joblib</samp></dd>
    <dt>snpeff_cache</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/annotation-cache/snpeff_cache/</samp></dd>
    <dt>snpeff_db</dt><dd><samp>GRCh38.105</samp></dd>
    <dt>target_beds</dt><dd><samp>s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/bed/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed,s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/bed/altera_v3_targets_coding_postQC_hg38_chr21.bed</samp></dd>
    <dt>vep_cache</dt><dd><samp>s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/annotation-cache/vep_cache/</samp></dd>
    <dt>vep_cache_version</dt><dd><samp>113</samp></dd>
    <dt>vep_genome</dt><dd><samp>GRCh38</samp></dd>
    <dt>vep_species</dt><dd><samp>homo_sapiens</samp></dd>
</dl>
<p style="font-size:110%"><b>Institutional config options</b></p>
<dl class="dl-horizontal">
    <dt>modules_testdata_base_path</dt><dd><samp>s3://natera-platform-sandbox/pipeline-inputs/test_sarek/</samp></dd>
</dl>
<p style="font-size:110%"><b>Generic options</b></p>
<dl class="dl-horizontal">
    <dt>task_job_queue</dt><dd><samp>Nextflow-OnDemand</samp></dd>
</dl>
<p style="font-size:110%"><b>Core Nextflow options</b></p>
<dl class="dl-horizontal">
    <dt>configFiles</dt><dd><samp><span style="color:#999999;">N/A</a></samp></dd>
    <dt>container</dt><dd><samp>[GERMLINE_CNV:292967571998.dkr.ecr.us-west-2.amazonaws.com/sarek/altera_cnv:0.5.0]</samp></dd>
    <dt>containerEngine</dt><dd><samp>docker</samp></dd>
    <dt>launchDir</dt><dd><samp>/code</samp></dd>
    <dt>profile</dt><dd><samp>docker,test_regression,eks</samp></dd>
    <dt>projectDir</dt><dd><samp>/tmp/home/.nextflow/assets/rd-platform/bioinformatics/nextflow/sarek</samp></dd>
    <dt>runName</dt><dd><samp>gitlab-sarek-build2797494-baseline-run-63551853</samp></dd>
    <dt>userName</dt><dd><samp>nextflow</samp></dd>
    <dt>workDir</dt><dd><samp>/natera-rnd-pltf-dev-nextflow-scratch-01/work</samp></dd>
</dl>


----------------------

Tool: Samtools Flagstat
Section: Percent mapped
Section description: Alignment metrics from <code>samtools stats</code>; mapped vs. unmapped reads vs. reads mapped with MQ0.
Section help text: For a set of samples that have come from the same multiplexed library,
similar numbers of reads for each sample are expected. Large differences in numbers might
indicate issues during the library preparation process. Whilst large differences in read
numbers may be controlled for in downstream processings (e.g. read count normalisation),
you may wish to consider whether the read depths achieved have fallen below recommended
levels depending on the applications.
Low alignment rates could indicate contamination of samples (e.g. adapter sequences),
low sequencing quality or other artefacts. These can be further investigated in the
sequence level QC (e.g. from FastQC).
Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple
locations in the reference sequence. This can be due to repetitive regions in the genome,
the presence of alternative contigs in the reference, or due to reads that are too short
to be uniquely mapped. These reads are often filtered out in downstream analyses.
Title: Samtools: stats: Alignment Scores

Plot type: bar plot
Values: # Reads

|Sample|Mapped (with MQ>0)|MQ0|Unmapped|
|---|---|---|---|
|Sig_18_tissue|10,830,424|1,479,224|78|
|Sig_18_Blood|2,171,401|307,164|19|
|HCC1395_tumor|4,647,507|701,775|34|
|HCC1395_BL|1,700,368|252,998|16|

----------------------

Tool: Samtools Flagstat
Section: Alignment stats
Section description: This module parses the output from <code>samtools stats</code>. All numbers in millions.
Title: Samtools: stats: Alignment Stats

Plot type: violin plot

Number of samples: 4

Metrics:
Total sequences - Total sequences
Mapped &amp; paired - Paired-end technology bit set + both mates mapped
Properly paired - Proper-pair bit set
Duplicated - PCR or optical duplicate bit set
QC Failed - QC Failed
Reads MQ0 - Reads mapped and MQ=0
Mapped bases (CIGAR) - Mapped bases (CIGAR)
Bases Trimmed - Bases Trimmed
Duplicated bases - Duplicated bases
Diff chromosomes - Pairs on different chromosomes
Other orientation - Pairs with other orientation
Inward pairs - Inward oriented pairs
Outward pairs - Outward oriented pairs

|Sample Name|Total sequences|Mapped &amp; paired|Properly paired|Duplicated|QC Failed|Reads MQ0|Mapped bases (CIGAR)|Bases Trimmed|Duplicated bases|Diff chromosomes|Other orientation|Inward pairs|Outward pairs|
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|HCC1395_BL|1.95|1.95|1.95|0.40|0.0|0.25|281.23|0.0|57.61|0.00|0.00|0.90|0.08|
|HCC1395_tumor|5.35|5.35|5.34|2.08|0.0|0.70|767.77|0.0|299.60|0.00|0.00|2.44|0.23|
|Sig_18_Blood|2.48|2.48|2.48|0.37|0.0|0.31|358.47|0.0|54.29|0.00|0.00|1.15|0.09|
|Sig_18_tissue|12.31|12.31|12.30|3.88|0.0|1.48|1734.78|0.0|546.37|0.00|0.00|5.39|0.76|

----------------------

Tool: Mosdepth
Section: Cumulative coverage distribution
Section description: Proportion of bases in the reference genome with, at least, a given depth of coverage. Note that for 4 samples, a BED file was provided, so the data was calculated across those regions. For 4 samples, it's calculated across the entire genome length. 4 samples have both global and region reports, and we are showing the data for regions
Section help text: For a set of DNA or RNA reads mapped to a reference sequence, such as a genome
or transcriptome, the depth of coverage at a given base position is the number
of high-quality reads that map to the reference at that position, while the
breadth of coverage is the fraction of the reference sequence to which reads
have been mapped with at least a given depth of coverage
(<a href="https://doi.org/10.1038/nrg3642" target="_blank">Sims et al. 2014</a>).
Defining coverage breadth in terms of coverage depth is useful, because
sequencing experiments typically require a specific minimum depth of coverage
over the region of interest (<a href="https://doi.org/10.1038/nrg3642"
target="_blank">Sims et al. 2014</a>), so the extent of the reference sequence
that is amenable to analysis is constrained to lie within regions that have
sufficient depth. With inadequate sequencing breadth, it can be difficult to
distinguish the absence of a biological feature (such as a gene) from a lack
of data (<a href="https://doi.org/10.1101/gr.7050807" target="_blank">Green 2007</a>).
For increasing coverage depths (<em>1&#215;, 2&#215;, &#8230;, N&#215;</em>),
coverage breadth is calculated as the percentage of the reference
sequence that is covered by at least that number of reads, then plots
coverage breadth (y-axis) against coverage depth (x-axis). This plot
shows the relationship between sequencing depth and breadth for each read
dataset, which can be used to gauge, for example, the likely effect of a
minimum depth filter on the fraction of a genome available for analysis.
Title: Mosdepth: Cumulative coverage distribution

Plot type: x/y line
X axis: Cumulative Coverage (X)
Y axis: % bases in genome/regions covered by at least X reads

Samples: HCC1395_BL, HCC1395_tumor, Sig_18_Blood, Sig_18_tissue

Y values are in %

X values are in X

HCC1395_BL 0: 100, 2: 100, 5: 100, 7: 100, 9: 100, 12: 100, 14: 100, 16: 100, 19: 100, 21: 100, 23: 100, 26: 100, 28: 100, 30: 100, 32: 100, 35: 100, 37: 100, 39: 99, 42: 99, 44: 99, 46: 99, 49: 99, 51: 98, 53: 98, 56: 98, 58: 97, 60: 97, 63: 96, 65: 95, 67: 95, 70: 94, 72: 93, 74: 92, 77: 91, 79: 90, 81: 89, 83: 89, 86: 87, 88: 86, 90: 85, 93: 83, 95: 82, 97: 81, 100: 79, 102: 78, 104: 77, 107: 75, 109: 74, 111: 73, 114: 71, 116: 70, 118: 68, 121: 67, 123: 65, 125: 64, 128: 62, 130: 61, 132: 60, 134: 59, 137: 56, 139: 56, 141: 54, 144: 53, 146: 51, 148: 50, 151: 49, 153: 48, 155: 47, 158: 45, 160: 44, 162: 43, 165: 42, 167: 41, 169: 40, 172: 38, 174: 37, 176: 37, 179: 35, 181: 35, 183: 34, 185: 33, 188: 32, 190: 31, 192: 30, 195: 28, 197: 28, 199: 28, 202: 27, 204: 26, 206: 26, 209: 25, 211: 25, 213: 24, 216: 23, 218: 23, 220: 22, 223: 22, 225: 21, 227: 21, 230: 20, 232: 20, 234: 20, 237: 19, 239: 19, 241: 19, 243: 18, 246: 18, 248: 18, 250: 18, 253: 17, 255: 17, 257: 17, 260: 17, 262: 16, 264: 16, 267: 16, 269: 16, 271: 16, 274: 16, 276: 16, 278: 15, 281: 15, 283: 15, 285: 15, 288: 15, 290: 15, 292: 15, 294: 15, 297: 15, 299: 15, 301: 15, 304: 15, 306: 14, 308: 14, 311: 14, 313: 14, 315: 14, 318: 14, 320: 14, 322: 14, 325: 14, 327: 14, 329: 14, 332: 14, 334: 14, 336: 14, 339: 14, 341: 14, 343: 13, 345: 13, 348: 13, 350: 13, 352: 13, 355: 13, 357: 13, 359: 13, 362: 13, 364: 13, 366: 13, 369: 13, 371: 13, 373: 13, 376: 13, 378: 13, 380: 13, 383: 13, 385: 13, 387: 13, 390: 13, 392: 13, 394: 13, 396: 13, 399: 13, 401: 13, 403: 13, 406: 13, 408: 13, 410: 13, 413: 13, 415: 12, 417: 12, 420: 12, 422: 12, 424: 12, 427: 12, 429: 12, 431: 12, 434: 12, 436: 12, 438: 12, 441: 12, 443: 12, 445: 12, 447: 12, 450: 12, 452: 12, 454: 12, 457: 12, 459: 12, 461: 12, 464: 12, 466: 12, 468: 12, 471: 12, 473: 12, 475: 12, 478: 12, 480: 12, 482: 12, 485: 12, 487: 12, 489: 12, 492: 12, 494: 12, 496: 12, 499: 12, 501: 12, 503: 12, 505: 12, 508: 12, 510: 12, 512: 12, 515: 12, 517: 12, 519: 11, 522: 11, 524: 11, 526: 11, 529: 11, 531: 11, 533: 11, 536: 11, 538: 11, 540: 11, 543: 11, 545: 11, 547: 11, 550: 11, 552: 11, 554: 11, 556: 11, 559: 11, 561: 11, 563: 11, 566: 11, 568: 11, 570: 11, 573: 11, 575: 11, 577: 11, 580: 11, 582: 11, 584: 11, 587: 11, 589: 11, 591: 11, 594: 11, 596: 11, 598: 11, 601: 11, 603: 11, 605: 11, 607: 11, 610: 10, 612: 10, 614: 10, 617: 10, 619: 10, 621: 10, 624: 10, 626: 10, 628: 10, 631: 10, 633: 10, 635: 10, 638: 10, 640: 10, 642: 10, 645: 10, 647: 10, 649: 10, 652: 10, 654: 10, 656: 10, 658: 10, 661: 10, 663: 9, 665: 9, 668: 9, 670: 9, 672: 9, 675: 9, 677: 9, 679: 9, 682: 9, 684: 9, 686: 9, 689: 9, 691: 9, 693: 9, 696: 9, 698: 9, 700: 9, 703: 9, 705: 9, 707: 9, 710: 9, 712: 9, 714: 9, 716: 9, 719: 9, 721: 8, 723: 8, 726: 8, 728: 8, 730: 8, 733: 8, 735: 8, 737: 8, 740: 8, 742: 8, 744: 8, 747: 8, 749: 8, 751: 8, 754: 8, 756: 8, 758: 8, 761: 8, 763: 8, 765: 8, 767: 8, 770: 8, 772: 8, 774: 8, 777: 8, 779: 8, 781: 7, 784: 7, 786: 7, 788: 7, 791: 7, 793: 7, 795: 7, 798: 7, 800: 7, 802: 7, 805: 7, 807: 7, 809: 7, 812: 7, 814: 7, 816: 7, 818: 7, 821: 7, 823: 7, 825: 7, 828: 6, 830: 6, 832: 6, 835: 6, 837: 6, 839: 6, 842: 6, 844: 6, 846: 6, 849: 6, 851: 6, 853: 6, 856: 6, 858: 6, 860: 6, 863: 6, 865: 6, 867: 6, 869: 5, 872: 5, 874: 5, 876: 5, 879: 5, 881: 5, 883: 5, 886: 5, 888: 5, 890: 5, 893: 5, 895: 5, 897: 5, 900: 5, 902: 5, 904: 5, 907: 5, 909: 5, 911: 5, 914: 5, 916: 4, 918: 4, 920: 4, 923: 4, 925: 4, 927: 4, 930: 4, 932: 4, 934: 4, 937: 4, 939: 4, 941: 4, 944: 4, 946: 4, 948: 4, 951: 4, 953: 4, 955: 4, 958: 4, 960: 4, 962: 3, 965: 3, 967: 3, 969: 3, 972: 3, 974: 3, 976: 3, 978: 3, 981: 3, 983: 3, 985: 3, 988: 3, 990: 3, 992: 3, 995: 3, 997: 3, 999: 3, 1,002: 3, 1,004: 3, 1,006: 3, 1,009: 3, 1,011: 3, 1,013: 2, 1,016: 2, 1,018: 2, 1,020: 2, 1,023: 2, 1,025: 2, 1,027: 2, 1,029: 2, 1,032: 2, 1,034: 2, 1,036: 2, 1,039: 2, 1,041: 2, 1,043: 2, 1,046: 2, 1,048: 2, 1,050: 2, 1,053: 2, 1,055: 2, 1,057: 2, 1,060: 2, 1,062: 2, 1,064: 2, 1,067: 2, 1,069: 2, 1,071: 2, 1,074: 1, 1,076: 1, 1,078: 1, 1,080: 1, 1,083: 1, 1,085: 1, 1,087: 1, 1,090: 1, 1,092: 1, 1,094: 1, 1,097: 1, 1,099: 1, 1,101: 1, 1,104: 1, 1,106: 1, 1,108: 1, 1,111: 1, 1,113: 1, 1,115: 1, 1,118: 1, 1,120: 1, 1,122: 1, 1,125: 1, 1,127: 1, 1,129: 1, 1,131: 1, 1,134: 1, 1,136: 1, 1,138: 1, 1,141: 1, 1,143: 1, 1,145: 1, 1,148: 1, 1,150: 1, 1,152: 1, 1,155: 1, 1,157: 1

HCC1395_tumor 0: 100, 3: 100, 7: 100, 10: 100, 13: 100, 16: 100, 20: 100, 23: 100, 26: 100, 30: 100, 33: 100, 36: 100, 39: 100, 43: 100, 46: 100, 49: 100, 53: 100, 56: 100, 59: 100, 63: 100, 66: 100, 69: 100, 72: 99, 76: 99, 79: 99, 82: 99, 86: 99, 89: 99, 92: 99, 95: 99, 99: 99, 102: 98, 105: 98, 109: 98, 112: 98, 115: 97, 118: 97, 122: 97, 125: 97, 128: 96, 132: 96, 135: 96, 138: 95, 141: 95, 145: 95, 148: 94, 151: 94, 155: 93, 158: 93, 161: 92, 165: 92, 168: 91, 171: 91, 174: 90, 178: 89, 181: 89, 184: 88, 188: 87, 191: 87, 194: 86, 197: 85, 201: 84, 204: 83, 207: 83, 211: 82, 214: 81, 217: 80, 220: 79, 224: 78, 227: 77, 230: 77, 234: 75, 237: 75, 240: 74, 244: 73, 247: 72, 250: 71, 253: 70, 257: 69, 260: 69, 263: 68, 267: 67, 270: 66, 273: 65, 276: 64, 280: 63, 283: 62, 286: 62, 290: 61, 293: 60, 296: 59, 299: 57, 303: 56, 306: 56, 309: 56, 313: 55, 316: 54, 319: 53, 322: 53, 326: 52, 329: 51, 332: 50, 336: 49, 339: 49, 342: 48, 346: 47, 349: 46, 352: 45, 355: 45, 359: 44, 362: 43, 365: 43, 369: 42, 372: 41, 375: 41, 378: 40, 382: 39, 385: 39, 388: 38, 392: 37, 395: 37, 398: 36, 401: 36, 405: 35, 408: 34, 411: 34, 415: 33, 418: 33, 421: 32, 424: 32, 428: 31, 431: 31, 434: 30, 438: 30, 441: 28, 444: 28, 448: 28, 451: 28, 454: 27, 457: 27, 461: 26, 464: 26, 467: 26, 471: 25, 474: 25, 477: 24, 480: 24, 484: 24, 487: 23, 490: 23, 494: 23, 497: 23, 500: 22, 503: 22, 507: 22, 510: 21, 513: 21, 517: 21, 520: 21, 523: 20, 526: 20, 530: 20, 533: 20, 536: 19, 540: 19, 543: 19, 546: 19, 550: 19, 553: 19, 556: 18, 559: 18, 563: 18, 566: 18, 569: 18, 573: 17, 576: 17, 579: 17, 582: 17, 586: 17, 589: 17, 592: 17, 596: 16, 599: 16, 602: 16, 605: 16, 609: 16, 612: 16, 615: 16, 619: 16, 622: 16, 625: 16, 629: 15, 632: 15, 635: 15, 638: 15, 642: 15, 645: 15, 648: 15, 652: 15, 655: 15, 658: 15, 661: 15, 665: 14, 668: 14, 671: 14, 675: 14, 678: 14, 681: 14, 684: 14, 688: 14, 691: 14, 694: 14, 698: 13, 701: 13, 704: 13, 707: 13, 711: 13, 714: 13, 717: 13, 721: 13, 724: 13, 727: 13, 731: 13, 734: 13, 737: 13, 740: 13, 744: 12, 747: 12, 750: 12, 754: 12, 757: 12, 760: 12, 763: 12, 767: 12, 770: 12, 773: 12, 777: 12, 780: 12, 783: 12, 786: 12, 790: 12, 793: 12, 796: 12, 800: 12, 803: 12, 806: 12, 809: 12, 813: 12, 816: 12, 819: 12, 823: 12, 826: 12, 829: 12, 833: 12, 836: 12, 839: 12, 842: 11, 846: 11, 849: 11, 852: 11, 856: 11, 859: 11, 862: 11, 865: 11, 869: 11, 872: 11, 875: 11, 879: 11, 882: 11, 885: 11, 888: 11, 892: 11, 895: 11, 898: 11, 902: 11, 905: 11, 908: 11, 911: 11, 915: 11, 918: 11, 921: 11, 925: 11, 928: 11, 931: 11, 935: 11, 938: 11, 941: 11, 944: 11, 948: 11, 951: 10, 954: 10, 958: 10, 961: 10, 964: 10, 967: 10, 971: 10, 974: 10, 977: 10, 981: 10, 984: 10, 987: 10, 990: 10, 994: 10, 997: 10, 1,000: 10, 1,004: 10, 1,007: 10, 1,010: 10, 1,013: 10, 1,017: 10, 1,020: 10, 1,023: 10, 1,027: 10, 1,030: 10, 1,033: 10, 1,037: 10, 1,040: 10, 1,043: 10, 1,046: 10, 1,050: 10, 1,053: 10, 1,056: 9, 1,060: 9, 1,063: 9, 1,066: 9, 1,069: 9, 1,073: 9, 1,076: 9, 1,079: 9, 1,083: 9, 1,086: 9, 1,089: 9, 1,092: 9, 1,096: 9, 1,099: 9, 1,102: 9, 1,106: 9, 1,109: 9, 1,112: 9, 1,116: 9, 1,119: 9, 1,122: 9, 1,125: 9, 1,129: 9, 1,132: 9, 1,135: 8, 1,139: 8, 1,142: 8, 1,145: 8, 1,148: 8, 1,152: 8, 1,155: 8, 1,158: 8, 1,162: 8, 1,165: 8, 1,168: 8, 1,171: 8, 1,175: 8, 1,178: 8, 1,181: 8, 1,185: 8, 1,188: 8, 1,191: 8, 1,194: 8, 1,198: 8, 1,201: 8, 1,204: 8, 1,208: 8, 1,211: 8, 1,214: 8, 1,218: 7, 1,221: 7, 1,224: 7, 1,227: 7, 1,231: 7, 1,234: 7, 1,237: 7, 1,241: 7, 1,244: 7, 1,247: 7, 1,250: 7, 1,254: 7, 1,257: 7, 1,260: 7, 1,264: 7, 1,267: 7, 1,270: 7, 1,273: 7, 1,277: 7, 1,280: 7, 1,283: 7, 1,287: 7, 1,290: 7, 1,293: 7, 1,296: 7, 1,300: 6, 1,303: 6, 1,306: 6, 1,310: 6, 1,313: 6, 1,316: 6, 1,320: 6, 1,323: 6, 1,326: 6, 1,329: 6, 1,333: 6, 1,336: 6, 1,339: 6, 1,343: 6, 1,346: 6, 1,349: 6, 1,352: 6, 1,356: 5, 1,359: 5, 1,362: 5, 1,366: 5, 1,369: 5, 1,372: 5, 1,375: 5, 1,379: 5, 1,382: 5, 1,385: 5, 1,389: 5, 1,392: 5, 1,395: 5, 1,398: 5, 1,402: 5, 1,405: 5, 1,408: 5, 1,412: 4, 1,415: 4, 1,418: 4, 1,422: 4, 1,425: 4, 1,428: 4, 1,431: 4, 1,435: 4, 1,438: 4, 1,441: 4, 1,445: 4, 1,448: 4, 1,451: 4, 1,454: 4, 1,458: 3, 1,461: 3, 1,464: 3, 1,468: 3, 1,471: 3, 1,474: 3, 1,477: 3, 1,481: 3, 1,484: 3, 1,487: 3, 1,491: 3, 1,494: 3, 1,497: 3, 1,501: 3, 1,504: 3, 1,507: 3, 1,510: 3, 1,514: 2, 1,517: 2, 1,520: 2, 1,524: 2, 1,527: 2, 1,530: 2, 1,533: 2, 1,537: 2, 1,540: 2, 1,543: 2, 1,547: 2, 1,550: 2, 1,553: 2, 1,556: 2, 1,560: 2, 1,563: 2, 1,566: 1, 1,570: 1, 1,573: 1, 1,576: 1, 1,579: 1, 1,583: 1, 1,586: 1, 1,589: 1, 1,593: 1, 1,596: 1, 1,599: 1, 1,603: 1, 1,606: 1, 1,609: 1, 1,612: 1, 1,616: 1, 1,619: 1, 1,622: 1, 1,626: 1, 1,629: 1, 1,632: 1, 1,635: 1, 1,639: 1, 1,642: 1

Sig_18_Blood 0: 100, 4: 100, 7: 100, 11: 100, 15: 100, 19: 100, 22: 100, 26: 100, 30: 100, 34: 100, 37: 100, 41: 100, 45: 100, 48: 100, 52: 99, 56: 99, 60: 99, 63: 99, 67: 99, 71: 98, 74: 98, 78: 97, 82: 97, 86: 96, 89: 95, 93: 94, 97: 93, 101: 92, 104: 91, 108: 90, 112: 88, 115: 87, 119: 85, 123: 84, 127: 82, 130: 80, 134: 79, 138: 77, 141: 75, 145: 73, 149: 71, 153: 69, 156: 68, 160: 66, 164: 64, 168: 62, 171: 60, 175: 59, 179: 56, 182: 55, 186: 53, 190: 52, 194: 50, 197: 49, 201: 47, 205: 46, 209: 44, 212: 43, 216: 41, 220: 40, 223: 39, 227: 37, 231: 36, 235: 35, 238: 34, 242: 33, 246: 32, 249: 31, 253: 30, 257: 28, 261: 28, 264: 27, 268: 26, 272: 25, 276: 25, 279: 24, 283: 23, 287: 23, 290: 22, 294: 22, 298: 21, 302: 21, 305: 20, 309: 20, 313: 19, 316: 19, 320: 19, 324: 18, 328: 18, 331: 18, 335: 18, 339: 17, 343: 17, 346: 17, 350: 17, 354: 17, 357: 16, 361: 16, 365: 16, 369: 16, 372: 16, 376: 16, 380: 15, 384: 15, 387: 15, 391: 15, 395: 15, 398: 15, 402: 15, 406: 15, 410: 14, 413: 14, 417: 14, 421: 14, 424: 14, 428: 14, 432: 14, 436: 14, 439: 14, 443: 14, 447: 14, 451: 14, 454: 14, 458: 14, 462: 14, 465: 14, 469: 14, 473: 14, 477: 14, 480: 13, 484: 13, 488: 13, 491: 13, 495: 13, 499: 13, 503: 13, 506: 13, 510: 13, 514: 13, 518: 13, 521: 13, 525: 13, 529: 13, 532: 13, 536: 13, 540: 13, 544: 13, 547: 13, 551: 13, 555: 13, 559: 13, 562: 13, 566: 13, 570: 13, 573: 13, 577: 13, 581: 13, 585: 13, 588: 13, 592: 13, 596: 13, 599: 13, 603: 12, 607: 12, 611: 12, 614: 12, 618: 12, 622: 12, 626: 12, 629: 12, 633: 12, 637: 12, 640: 12, 644: 12, 648: 12, 652: 12, 655: 12, 659: 12, 663: 12, 666: 12, 670: 12, 674: 12, 678: 12, 681: 12, 685: 12, 689: 12, 693: 12, 696: 12, 700: 12, 704: 12, 707: 12, 711: 12, 715: 12, 719: 12, 722: 12, 726: 12, 730: 12, 734: 12, 737: 12, 741: 12, 745: 12, 748: 12, 752: 12, 756: 12, 760: 12, 763: 11, 767: 11, 771: 11, 774: 11, 778: 11, 782: 11, 786: 11, 789: 11, 793: 11, 797: 11, 801: 11, 804: 11, 808: 11, 812: 11, 815: 11, 819: 11, 823: 11, 827: 11, 830: 11, 834: 11, 838: 11, 841: 11, 845: 11, 849: 11, 853: 11, 856: 11, 860: 11, 864: 11, 868: 11, 871: 11, 875: 11, 879: 11, 882: 11, 886: 11, 890: 11, 894: 11, 897: 11, 901: 11, 905: 10, 909: 10, 912: 10, 916: 10, 920: 10, 923: 10, 927: 10, 931: 10, 935: 10, 938: 10, 942: 10, 946: 10, 949: 10, 953: 10, 957: 10, 961: 10, 964: 10, 968: 10, 972: 10, 976: 10, 979: 10, 983: 10, 987: 10, 990: 10, 994: 9, 998: 9, 1,002: 9, 1,005: 9, 1,009: 9, 1,013: 9, 1,017: 9, 1,020: 9, 1,024: 9, 1,028: 9, 1,031: 9, 1,035: 9, 1,039: 9, 1,043: 9, 1,046: 9, 1,050: 9, 1,054: 9, 1,057: 9, 1,061: 9, 1,065: 9, 1,069: 9, 1,072: 9, 1,076: 9, 1,080: 9, 1,084: 9, 1,087: 9, 1,091: 9, 1,095: 9, 1,098: 9, 1,102: 8, 1,106: 8, 1,110: 8, 1,113: 8, 1,117: 8, 1,121: 8, 1,124: 8, 1,128: 8, 1,132: 8, 1,136: 8, 1,139: 8, 1,143: 8, 1,147: 8, 1,151: 8, 1,154: 8, 1,158: 8, 1,162: 8, 1,165: 8, 1,169: 8, 1,173: 8, 1,177: 8, 1,180: 8, 1,184: 8, 1,188: 8, 1,192: 8, 1,195: 8, 1,199: 8, 1,203: 8, 1,206: 8, 1,210: 8, 1,214: 8, 1,218: 8, 1,221: 8, 1,225: 7, 1,229: 7, 1,232: 7, 1,236: 7, 1,240: 7, 1,244: 7, 1,247: 7, 1,251: 7, 1,255: 7, 1,259: 7, 1,262: 7, 1,266: 7, 1,270: 7, 1,273: 7, 1,277: 7, 1,281: 7, 1,285: 7, 1,288: 7, 1,292: 7, 1,296: 7, 1,299: 7, 1,303: 7, 1,307: 7, 1,311: 7, 1,314: 7, 1,318: 6, 1,322: 6, 1,326: 6, 1,329: 6, 1,333: 6, 1,337: 6, 1,340: 6, 1,344: 6, 1,348: 6, 1,352: 6, 1,355: 6, 1,359: 6, 1,363: 6, 1,367: 6, 1,370: 6, 1,374: 6, 1,378: 6, 1,381: 6, 1,385: 6, 1,389: 6, 1,393: 5, 1,396: 5, 1,400: 5, 1,404: 5, 1,407: 5, 1,411: 5, 1,415: 5, 1,419: 5, 1,422: 5, 1,426: 5, 1,430: 5, 1,434: 5, 1,437: 5, 1,441: 5, 1,445: 5, 1,448: 5, 1,452: 5, 1,456: 5, 1,460: 5, 1,463: 4, 1,467: 4, 1,471: 4, 1,474: 4, 1,478: 4, 1,482: 4, 1,486: 4, 1,489: 4, 1,493: 4, 1,497: 4, 1,501: 4, 1,504: 4, 1,508: 4, 1,512: 4, 1,515: 4, 1,519: 4, 1,523: 4, 1,527: 4, 1,530: 4, 1,534: 4, 1,538: 3, 1,542: 3, 1,545: 3, 1,549: 3, 1,553: 3, 1,556: 3, 1,560: 3, 1,564: 3, 1,568: 3, 1,571: 3, 1,575: 3, 1,579: 3, 1,582: 3, 1,586: 3, 1,590: 3, 1,594: 3, 1,597: 3, 1,601: 3, 1,605: 2, 1,609: 2, 1,612: 2, 1,616: 2, 1,620: 2, 1,623: 2, 1,627: 2, 1,631: 2, 1,635: 2, 1,638: 2, 1,642: 2, 1,646: 2, 1,649: 2, 1,653: 2, 1,657: 2, 1,661: 2, 1,664: 2, 1,668: 2, 1,672: 2, 1,676: 2, 1,679: 2, 1,683: 2, 1,687: 2, 1,690: 1, 1,694: 1, 1,698: 1, 1,702: 1, 1,705: 1, 1,709: 1, 1,713: 1, 1,717: 1, 1,720: 1, 1,724: 1, 1,728: 1, 1,731: 1, 1,735: 1, 1,739: 1, 1,743: 1, 1,746: 1, 1,750: 1, 1,754: 1, 1,757: 1, 1,761: 1, 1,765: 1, 1,769: 1, 1,772: 1, 1,776: 1, 1,780: 1, 1,784: 1, 1,787: 1, 1,791: 1, 1,795: 1, 1,798: 1, 1,802: 1, 1,806: 1, 1,810: 1, 1,813: 1, 1,817: 1, 1,821: 1, 1,824: 1, 1,828: 1, 1,832: 1, 1,836: 1, 1,839: 1, 1,843: 1, 1,847: 1, 1,851: 1, 1,854: 1, 1,858: 1

Sig_18_tissue 0: 100, 11: 100, 22: 100, 34: 100, 45: 100, 56: 100, 67: 100, 79: 100, 90: 100, 101: 100, 112: 100, 123: 100, 135: 100, 146: 100, 157: 100, 168: 100, 180: 99, 191: 99, 202: 99, 213: 99, 225: 99, 236: 99, 247: 98, 258: 98, 269: 98, 281: 97, 292: 97, 303: 96, 314: 96, 326: 95, 337: 94, 348: 94, 359: 93, 370: 92, 382: 91, 393: 91, 404: 90, 415: 89, 427: 88, 438: 87, 449: 86, 460: 85, 472: 84, 483: 83, 494: 82, 505: 81, 516: 80, 528: 79, 539: 78, 550: 77, 561: 76, 573: 75, 584: 74, 595: 73, 606: 72, 617: 71, 629: 70, 640: 69, 651: 68, 662: 67, 674: 66, 685: 65, 696: 63, 707: 62, 718: 61, 730: 60, 741: 59, 752: 57, 763: 56, 775: 56, 786: 54, 797: 53, 808: 52, 820: 51, 831: 50, 842: 49, 853: 48, 864: 47, 876: 46, 887: 45, 898: 45, 909: 44, 921: 43, 932: 42, 943: 41, 954: 40, 965: 39, 977: 39, 988: 38, 999: 37, 1,010: 36, 1,022: 36, 1,033: 35, 1,044: 34, 1,055: 34, 1,067: 33, 1,078: 32, 1,089: 32, 1,100: 31, 1,111: 30, 1,123: 30, 1,134: 28, 1,145: 28, 1,156: 28, 1,168: 28, 1,179: 27, 1,190: 27, 1,201: 26, 1,212: 26, 1,224: 25, 1,235: 25, 1,246: 25, 1,257: 24, 1,269: 24, 1,280: 23, 1,291: 23, 1,302: 23, 1,313: 22, 1,325: 22, 1,336: 22, 1,347: 21, 1,358: 21, 1,370: 21, 1,381: 20, 1,392: 20, 1,403: 20, 1,415: 20, 1,426: 19, 1,437: 19, 1,448: 19, 1,459: 19, 1,471: 18, 1,482: 18, 1,493: 18, 1,504: 18, 1,516: 18, 1,527: 17, 1,538: 17, 1,549: 17, 1,560: 17, 1,572: 17, 1,583: 17, 1,594: 16, 1,605: 16, 1,617: 16, 1,628: 16, 1,639: 16, 1,650: 16, 1,662: 16, 1,673: 15, 1,684: 15, 1,695: 15, 1,706: 15, 1,718: 15, 1,729: 15, 1,740: 15, 1,751: 15, 1,763: 15, 1,774: 15, 1,785: 14, 1,796: 14, 1,807: 14, 1,819: 14, 1,830: 14, 1,841: 14, 1,852: 14, 1,864: 14, 1,875: 14, 1,886: 14, 1,897: 14, 1,908: 14, 1,920: 14, 1,931: 14, 1,942: 14, 1,953: 14, 1,965: 13, 1,976: 13, 1,987: 13, 1,998: 13, 2,010: 13, 2,021: 13, 2,032: 13, 2,043: 13, 2,054: 13, 2,066: 13, 2,077: 13, 2,088: 13, 2,099: 13, 2,111: 13, 2,122: 13, 2,133: 13, 2,144: 13, 2,155: 13, 2,167: 13, 2,178: 13, 2,189: 13, 2,200: 13, 2,212: 12, 2,223: 12, 2,234: 12, 2,245: 12, 2,257: 12, 2,268: 12, 2,279: 12, 2,290: 12, 2,301: 12, 2,313: 12, 2,324: 12, 2,335: 12, 2,346: 12, 2,358: 12, 2,369: 12, 2,380: 12, 2,391: 12, 2,402: 12, 2,414: 12, 2,425: 11, 2,436: 11, 2,447: 11, 2,459: 11, 2,470: 11, 2,481: 11, 2,492: 11, 2,503: 11, 2,515: 11, 2,526: 11, 2,537: 11, 2,548: 11, 2,560: 11, 2,571: 11, 2,582: 11, 2,593: 11, 2,605: 11, 2,616: 11, 2,627: 11, 2,638: 11, 2,649: 11, 2,661: 11, 2,672: 11, 2,683: 10, 2,694: 10, 2,706: 10, 2,717: 10, 2,728: 10, 2,739: 10, 2,750: 10, 2,762: 10, 2,773: 10, 2,784: 10, 2,795: 10, 2,807: 10, 2,818: 10, 2,829: 10, 2,840: 10, 2,852: 10, 2,863: 10, 2,874: 10, 2,885: 10, 2,896: 10, 2,908: 10, 2,919: 10, 2,930: 10, 2,941: 10, 2,953: 10, 2,964: 10, 2,975: 9, 2,986: 9, 2,997: 9, 3,009: 9, 3,020: 9, 3,031: 9, 3,042: 9, 3,054: 9, 3,065: 9, 3,076: 9, 3,087: 9, 3,099: 9, 3,110: 9, 3,121: 9, 3,132: 9, 3,143: 9, 3,155: 9, 3,166: 9, 3,177: 9, 3,188: 9, 3,200: 9, 3,211: 9, 3,222: 9, 3,233: 9, 3,244: 9, 3,256: 9, 3,267: 9, 3,278: 9, 3,289: 9, 3,301: 8, 3,312: 8, 3,323: 8, 3,334: 8, 3,345: 8, 3,357: 8, 3,368: 8, 3,379: 8, 3,390: 8, 3,402: 8, 3,413: 8, 3,424: 8, 3,435: 8, 3,447: 8, 3,458: 8, 3,469: 8, 3,480: 8, 3,491: 8, 3,503: 8, 3,514: 8, 3,525: 8, 3,536: 8, 3,548: 8, 3,559: 8, 3,570: 8, 3,581: 8, 3,592: 8, 3,604: 8, 3,615: 8, 3,626: 8, 3,637: 8, 3,649: 8, 3,660: 7, 3,671: 7, 3,682: 7, 3,694: 7, 3,705: 7, 3,716: 7, 3,727: 7, 3,738: 7, 3,750: 7, 3,761: 7, 3,772: 7, 3,783: 7, 3,795: 7, 3,806: 7, 3,817: 7, 3,828: 7, 3,839: 7, 3,851: 7, 3,862: 7, 3,873: 7, 3,884: 7, 3,896: 7, 3,907: 7, 3,918: 6, 3,929: 6, 3,940: 6, 3,952: 6, 3,963: 6, 3,974: 6, 3,985: 6, 3,997: 6, 4,008: 6, 4,019: 6, 4,030: 6, 4,042: 6, 4,053: 6, 4,064: 6, 4,075: 6, 4,086: 6, 4,098: 6, 4,109: 6, 4,120: 6, 4,131: 6, 4,143: 6, 4,154: 6, 4,165: 6, 4,176: 6, 4,187: 6, 4,199: 6, 4,210: 5, 4,221: 5, 4,232: 5, 4,244: 5, 4,255: 5, 4,266: 5, 4,277: 5, 4,289: 5, 4,300: 5, 4,311: 5, 4,322: 5, 4,333: 5, 4,345: 5, 4,356: 5, 4,367: 5, 4,378: 5, 4,390: 5, 4,401: 5, 4,412: 5, 4,423: 5, 4,434: 5, 4,446: 5, 4,457: 5, 4,468: 5, 4,479: 5, 4,491: 5, 4,502: 5, 4,513: 5, 4,524: 4, 4,535: 4, 4,547: 4, 4,558: 4, 4,569: 4, 4,580: 4, 4,592: 4, 4,603: 4, 4,614: 4, 4,625: 4, 4,637: 4, 4,648: 4, 4,659: 4, 4,670: 4, 4,681: 4, 4,693: 4, 4,704: 4, 4,715: 4, 4,726: 4, 4,738: 4, 4,749: 4, 4,760: 4, 4,771: 3, 4,782: 3, 4,794: 3, 4,805: 3, 4,816: 3, 4,827: 3, 4,839: 3, 4,850: 3, 4,861: 3, 4,872: 3, 4,884: 3, 4,895: 3, 4,906: 3, 4,917: 3, 4,928: 3, 4,940: 3, 4,951: 3, 4,962: 3, 4,973: 3, 4,985: 3, 4,996: 3, 5,007: 3, 5,018: 2, 5,029: 2, 5,041: 2, 5,052: 2, 5,063: 2, 5,074: 2, 5,086: 2, 5,097: 2, 5,108: 2, 5,119: 2, 5,130: 2, 5,142: 2, 5,153: 2, 5,164: 2, 5,175: 2, 5,187: 2, 5,198: 2, 5,209: 2, 5,220: 2, 5,232: 2, 5,243: 2, 5,254: 2

----------------------

Tool: Mosdepth
Section: Average coverage per contig
Section description: Average coverage per contig or chromosome
Title: Mosdepth: Coverage per contig

Plot type: bar plot
Values: Average Coverage

|Sample|chr21|
|---|---|
|Sig_18_tissue|1,216 x|
|Sig_18_Blood|330 x|
|HCC1395_tumor|442 x|
|HCC1395_BL|231 x|

----------------------

Tool: Mosdepth
Section: XY coverage
Title: Mosdepth: chrXY coverage

Plot type: bar plot
Values: Coverage

|Sample|Chromosome X|Chromosome Y|
|---|---|---|
|Sig_18_tissue|50% X|50% X|
|Sig_18_Blood|50% X|50% X|
|HCC1395_tumor|50% X|50% X|
|HCC1395_BL|50% X|50% X|

----------------------

Tool: Bcftools
Section: Variant Substitution Types
Title: Bcftools Stats: Substitutions

Plot type: bar plot
Values: # Substitutions

|Sample|A>C|A>G|A>T|C>A|C>G|C>T|G>A|G>C|G>T|T>A|T>C|T>G|
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs|10|16|4|32|11|46|43|8|18|5|26|18|
|custom_Sig_18_tumor_normal.strelka.somatic_indels|0|0|0|0|0|0|0|0|0|0|0|0|
|custom_Sig_18_tumor_normal.manta.somatic_sv|0|0|0|0|0|0|0|0|0|0|0|0|
|custom_Sig_18_tumor_normal.manta.diploid_sv|0|0|0|0|0|0|0|0|0|0|0|0|
|Sig_18_Blood.deconflicted_germline|13|64|9|10|13|75|71|24|8|7|65|10|
|Sig_18_Blood|0|0|0|0|0|0|0|0|0|0|0|0|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs|12|17|3|53|16|48|58|13|38|2|32|8|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels|0|0|0|0|0|0|0|0|0|0|0|0|
|HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv|0|0|0|0|0|0|0|0|0|0|0|0|
|HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv|0|0|0|0|0|0|0|0|0|0|0|0|
|HCC1395_BL.deconflicted_germline|8|57|4|8|13|73|67|20|6|5|64|9|
|HCC1395_BL|0|0|0|0|0|0|0|0|0|0|0|0|

----------------------

Tool: Bcftools
Section: Variant Quality
Title: Bcftools Stats: Variant Quality Count

Plot type: x/y line
X axis: Quality
Y axis: Count

### Count SNP

Samples: HCC1395_BL.deconflicted_germline, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs, Sig_18_Blood.deconflicted_germline, custom_Sig_18_tumor_normal.manta.diploid_sv, custom_Sig_18_tumor_normal.strelka.somatic_indels, custom_Sig_18_tumor_normal.strelka.somatic_snvs

HCC1395_BL.deconflicted_germline 67: 1, 136: 1, 256: 1, 497: 1, 627: 1, 645: 1, 695: 1, 712: 1, 747: 1, 790: 1, 796: 1, 813: 1, 946: 1, 1,021: 2, 1,057: 1, 1,078: 1, 1,096: 1, 1,159: 1, 1,177: 1, 1,188: 1, 1,189: 1, 1,209: 1, 1,216: 1, 1,221: 1, 1,293: 1, 1,334: 1, 1,362: 1, 1,369: 1, 1,370: 1, 1,371: 1, 1,390: 1, 1,396: 1, 1,399: 1, 1,400: 1, 1,402: 1, 1,446: 1, 1,457: 1, 1,461: 1, 1,474: 0, 1,480: 0, 1,522: 1, 1,547: 0, 1,551: 1, 1,553: 1, 1,576: 1, 1,591: 1, 1,593: 1, 1,624: 1, 1,639: 1, 1,656: 1, 1,667: 1, 1,669: 1, 1,676: 1, 1,677: 1, 1,680: 1, 1,697: 1, 1,699: 1, 1,725: 1, 1,729: 1, 1,730: 1, 1,764: 1, 1,791: 1, 1,816: 1, 1,817: 1, 1,836: 1, 1,838: 1, 1,861: 0, 1,863: 1, 1,868: 1, 1,880: 1, 1,885: 1, 1,896: 1, 1,916: 1, 1,924: 1, 1,939: 1, 1,952: 1, 1,966: 1, 1,980: 1, 2,038: 1, 2,070: 1, 2,094: 1, 2,123: 1, 2,139: 1, 2,144: 1, 2,163: 1, 2,182: 1, 2,183: 1, 2,184: 1, 2,196: 1, 2,197: 1, 2,220: 1, 2,229: 1, 2,238: 1, 2,246: 1, 2,258: 1, 2,266: 1, 2,268: 1, 2,273: 1, 2,279: 1, 2,294: 1, 2,309: 1, 2,312: 1, 2,323: 1, 2,325: 1, 2,343: 1, 2,366: 1, 2,377: 1, 2,379: 1, 2,391: 1, 2,401: 1, 2,402: 1, 2,406: 1, 2,415: 1, 2,476: 1, 2,480: 1, 2,484: 1, 2,507: 0, 2,513: 1, 2,535: 1, 2,562: 1, 2,596: 1, 2,612: 1, 2,620: 1, 2,635: 1, 2,655: 1, 2,657: 1, 2,678: 1, 2,684: 1, 2,685: 1, 2,714: 1, 2,725: 1, 2,751: 1, 2,753: 1, 2,772: 1, 2,792: 1, 2,800: 1, 2,828: 1, 2,862: 1, 2,875: 1, 2,882: 1, 2,894: 1, 2,911: 1, 2,938: 1, 2,940: 1, 2,955: 1, 2,961: 1, 3,000: 1, 3,004: 1, 3,027: 1, 3,054: 1, 3,101: 1, 3,102: 1, 3,107: 1, 3,117: 1, 3,128: 1, 3,154: 1, 3,160: 1, 3,166: 1, 3,179: 1, 3,204: 1, 3,209: 1, 3,224: 1, 3,260: 1, 3,262: 1, 3,290: 1, 3,303: 0, 3,314: 1, 3,337: 1, 3,347: 2, 3,460: 1, 3,482: 1, 3,489: 1, 3,505: 1, 3,511: 1, 3,546: 1, 3,573: 1, 3,576: 1, 3,592: 1, 3,652: 1, 3,674: 1, 3,684: 1, 3,716: 1, 3,718: 1, 3,787: 1, 3,860: 1, 3,894: 1, 3,897: 1, 3,899: 1, 3,905: 1, 3,948: 1, 3,953: 1, 4,031: 1, 4,043: 1, 4,077: 1, 4,078: 1, 4,084: 1, 4,096: 1, 4,119: 1, 4,129: 1, 4,173: 1, 4,187: 1, 4,195: 1, 4,199: 1, 4,305: 1, 4,308: 1, 4,317: 1, 4,318: 1, 4,337: 1, 4,350: 1, 4,353: 1, 4,563: 0, 4,746: 1, 4,873: 1, 4,909: 1, 4,963: 1, 4,969: 0, 4,999: 1, 5,107: 2, 5,228: 1, 5,307: 1, 5,319: 1, 5,414: 1, 5,427: 1, 5,551: 0, 5,559: 1, 5,759: 0, 5,783: 1, 5,810: 1, 5,815: 1, 5,828: 1, 5,830: 1, 5,840: 1, 5,874: 1, 5,941: 1, 5,945: 1, 5,946: 1, 6,012: 0, 6,136: 1, 6,202: 1, 6,209: 1, 6,254: 1, 6,352: 0, 6,379: 1, 6,425: 1, 6,443: 1, 6,505: 1, 6,642: 1, 6,643: 1, 6,696: 1, 6,715: 1, 6,738: 1, 6,834: 1, 6,869: 2, 6,908: 1, 6,960: 1, 6,991: 1, 7,016: 1, 7,067: 1, 7,095: 1, 7,115: 1, 7,212: 1, 7,290: 1, 7,424: 1, 7,484: 1, 7,634: 1, 7,675: 1, 7,745: 1, 7,805: 1, 7,890: 1, 8,022: 1, 8,158: 1, 8,177: 1, 8,265: 1, 8,363: 1, 8,413: 1, 8,517: 0, 8,541: 1, 8,615: 1, 8,759: 1, 8,921: 1, 8,971: 1, 9,018: 1, 9,202: 1, 9,805: 1, 9,808: 1, 10,272: 1, 10,329: 1, 10,453: 1, 10,544: 1, 10,619: 1, 10,754: 1, 10,758: 1, 10,991: 1, 11,395: 1, 11,500: 0, 11,978: 0, 12,334: 1, 12,362: 1, 12,444: 1, 12,843: 1, 13,009: 1, 13,054: 1, 13,403: 1, 13,677: 1, 13,697: 1, 13,732: 1, 13,916: 1, 14,231: 2, 14,716: 1, 14,849: 1, 15,063: 1, 15,129: 1, 15,161: 1, 15,236: 1, 15,313: 1, 15,343: 1, 15,454: 1, 15,511: 1, 15,699: 1, 15,767: 1, 15,889: 1, 15,905: 1, 16,363: 1, 16,645: 1, 16,767: 1, 16,962: 2, 17,631: 1, 18,877: 0, 19,296: 1, 19,551: 1, 20,546: 1, 20,745: 1, 21,364: 0, 21,437: 0, 22,295: 1, 30,979: 1, 33,075: 1, 33,624: 1, 35,237: 1, 35,447: 1, 35,755: 1, 36,249: 1, 37,860: 1, 38,714: 1, 43,225: 1, 45,044: 1

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels 0: 0

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs 0: 300

Sig_18_Blood.deconflicted_germline 48: 1, 148: 0, 193: 0, 226: 1, 434: 1, 466: 1, 469: 1, 506: 1, 701: 1, 755: 1, 765: 0, 786: 1, 830: 1, 1,122: 1, 1,133: 1, 1,139: 1, 1,206: 1, 1,216: 1, 1,266: 1, 1,298: 1, 1,312: 1, 1,315: 1, 1,316: 1, 1,372: 1, 1,404: 1, 1,430: 1, 1,437: 1, 1,560: 1, 1,585: 1, 1,588: 1, 1,599: 1, 1,610: 1, 1,632: 1, 1,640: 1, 1,675: 1, 1,676: 1, 1,695: 0, 1,696: 1, 1,728: 1, 1,750: 1, 1,790: 1, 1,802: 1, 1,803: 1, 1,827: 0, 1,847: 1, 1,867: 1, 1,872: 0, 1,925: 1, 1,931: 1, 1,945: 1, 1,948: 1, 1,959: 1, 1,961: 1, 1,965: 1, 1,973: 1, 1,978: 1, 2,050: 0, 2,053: 1, 2,074: 1, 2,076: 1, 2,097: 0, 2,109: 1, 2,148: 1, 2,152: 1, 2,179: 1, 2,190: 1, 2,234: 1, 2,252: 1, 2,290: 0, 2,310: 1, 2,322: 1, 2,332: 1, 2,335: 0, 2,336: 1, 2,367: 1, 2,415: 1, 2,422: 1, 2,427: 1, 2,460: 1, 2,472: 1, 2,490: 1, 2,495: 1, 2,499: 1, 2,518: 1, 2,540: 2, 2,557: 1, 2,572: 1, 2,594: 1, 2,606: 1, 2,612: 1, 2,641: 1, 2,654: 1, 2,664: 1, 2,697: 1, 2,725: 1, 2,735: 1, 2,745: 1, 2,771: 1, 2,776: 1, 2,816: 1, 2,828: 0, 2,832: 1, 2,848: 1, 2,885: 1, 2,907: 1, 2,963: 1, 2,986: 1, 2,990: 1, 3,003: 1, 3,004: 1, 3,010: 1, 3,063: 1, 3,071: 1, 3,123: 1, 3,138: 1, 3,151: 1, 3,177: 1, 3,243: 1, 3,322: 1, 3,328: 1, 3,355: 1, 3,375: 1, 3,389: 1, 3,404: 1, 3,431: 1, 3,449: 1, 3,451: 1, 3,457: 1, 3,465: 1, 3,466: 1, 3,509: 1, 3,534: 1, 3,537: 1, 3,542: 1, 3,543: 1, 3,586: 1, 3,619: 1, 3,627: 1, 3,632: 1, 3,653: 1, 3,658: 1, 3,667: 1, 3,674: 1, 3,738: 1, 3,801: 1, 3,823: 1, 3,851: 1, 3,872: 2, 3,891: 1, 3,907: 1, 3,911: 1, 3,941: 0, 3,942: 1, 3,949: 1, 4,020: 1, 4,056: 1, 4,083: 1, 4,102: 1, 4,123: 1, 4,168: 1, 4,208: 1, 4,310: 1, 4,316: 1, 4,366: 1, 4,373: 1, 4,384: 1, 4,420: 1, 4,440: 1, 4,474: 1, 4,594: 1, 4,655: 1, 4,659: 1, 4,727: 1, 4,747: 1, 4,761: 1, 4,787: 1, 4,804: 1, 4,806: 1, 4,836: 1, 4,838: 1, 4,880: 1, 4,914: 1, 4,921: 1, 4,979: 1, 5,008: 1, 5,038: 1, 5,040: 1, 5,048: 1, 5,099: 1, 5,144: 1, 5,205: 1, 5,218: 1, 5,219: 1, 5,303: 1, 5,321: 1, 5,377: 1, 5,398: 1, 5,405: 1, 5,484: 1, 5,515: 1, 5,586: 1, 5,606: 1, 5,649: 1, 5,716: 1, 5,750: 1, 5,763: 1, 5,829: 1, 5,831: 1, 5,858: 1, 5,902: 2, 5,917: 1, 5,986: 1, 5,991: 1, 6,012: 1, 6,090: 1, 6,104: 1, 6,173: 1, 6,292: 1, 6,424: 1, 6,527: 1, 6,563: 1, 6,578: 1, 6,637: 2, 6,687: 1, 6,737: 1, 6,750: 1, 6,785: 1, 6,808: 1, 6,846: 1, 6,888: 1, 6,989: 1, 7,029: 1, 7,159: 1, 7,195: 1, 7,197: 1, 7,214: 1, 7,608: 1, 7,612: 1, 7,636: 0, 7,657: 1, 7,724: 1, 7,729: 1, 7,743: 1, 7,756: 1, 7,758: 1, 7,765: 1, 7,824: 1, 7,896: 1, 7,897: 1, 7,907: 1, 8,005: 1, 8,039: 1, 8,156: 1, 8,196: 1, 8,206: 1, 8,275: 0, 8,297: 1, 8,364: 0, 8,377: 1, 8,399: 1, 8,512: 1, 8,709: 0, 8,728: 1, 8,814: 1, 8,868: 1, 8,886: 1, 8,974: 1, 8,986: 1, 8,995: 1, 9,003: 1, 9,077: 1, 9,080: 1, 9,100: 1, 9,200: 1, 9,252: 1, 9,295: 1, 9,360: 2, 9,428: 1, 9,430: 1, 9,471: 1, 9,510: 1, 9,801: 1, 9,836: 1, 9,845: 1, 9,953: 0, 10,214: 1, 10,217: 1, 10,623: 1, 10,647: 1, 10,995: 1, 11,041: 1, 11,043: 1, 11,092: 1, 11,122: 1, 11,156: 1, 11,159: 1, 11,238: 1, 11,257: 1, 11,414: 1, 11,497: 1, 11,533: 1, 11,985: 1, 12,051: 1, 12,251: 1, 12,503: 1, 12,650: 1, 12,966: 1, 13,107: 0, 13,255: 1, 13,677: 1, 13,923: 1, 13,973: 1, 14,298: 1, 14,493: 1, 14,736: 1, 14,969: 1, 15,013: 1, 15,113: 1, 15,211: 1, 15,684: 1, 16,265: 1, 16,890: 2, 17,730: 0, 19,079: 1, 19,367: 1, 19,595: 1, 19,613: 1, 19,671: 1, 19,746: 1, 19,971: 1, 20,129: 1, 20,369: 1, 20,855: 1, 22,259: 1, 22,325: 1, 22,363: 1, 22,626: 1, 22,949: 1, 23,288: 0, 23,430: 1, 23,529: 1, 23,723: 1, 24,057: 1, 24,189: 1, 24,211: 1, 24,213: 1, 24,219: 1, 24,360: 1, 24,369: 1, 24,434: 1, 24,544: 1, 24,813: 1, 24,959: 1, 25,128: 1, 25,441: 1, 25,851: 1, 26,200: 0, 26,356: 1, 26,651: 1, 27,416: 1, 28,524: 0, 29,524: 1, 29,881: 1, 29,979: 1, 32,909: 1, 33,061: 1, 33,639: 0, 33,937: 1, 34,068: 1, 34,327: 1, 35,795: 0, 36,258: 1, 37,203: 1, 47,750: 1, 47,881: 1, 52,465: 1, 53,967: 1, 54,929: 1, 55,182: 1, 56,417: 1, 56,907: 1, 61,334: 1, 61,722: 1, 64,325: 1, 71,282: 1, 73,423: 1, 75,216: 1, 78,636: 0

custom_Sig_18_tumor_normal.manta.diploid_sv 597: 0, 999: 0

custom_Sig_18_tumor_normal.strelka.somatic_indels 0: 0

custom_Sig_18_tumor_normal.strelka.somatic_snvs 0: 237


### Count Transitions

Samples: HCC1395_BL.deconflicted_germline, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs, Sig_18_Blood.deconflicted_germline, custom_Sig_18_tumor_normal.manta.diploid_sv, custom_Sig_18_tumor_normal.strelka.somatic_indels, custom_Sig_18_tumor_normal.strelka.somatic_snvs

HCC1395_BL.deconflicted_germline 67: 1, 136: 1, 256: 1, 497: 0, 627: 1, 645: 1, 695: 1, 712: 1, 747: 1, 790: 1, 796: 0, 813: 0, 946: 1, 1,021: 1, 1,057: 1, 1,078: 1, 1,096: 0, 1,159: 1, 1,177: 1, 1,188: 1, 1,189: 1, 1,209: 1, 1,216: 1, 1,221: 0, 1,293: 1, 1,334: 1, 1,362: 0, 1,369: 1, 1,370: 1, 1,371: 1, 1,390: 1, 1,396: 1, 1,399: 1, 1,400: 0, 1,402: 1, 1,446: 1, 1,457: 1, 1,461: 1, 1,474: 0, 1,480: 0, 1,522: 1, 1,547: 0, 1,551: 1, 1,553: 0, 1,576: 0, 1,591: 1, 1,593: 0, 1,624: 1, 1,639: 1, 1,656: 1, 1,667: 1, 1,669: 1, 1,676: 1, 1,677: 1, 1,680: 1, 1,697: 1, 1,699: 1, 1,725: 1, 1,729: 0, 1,730: 1, 1,764: 0, 1,791: 0, 1,816: 1, 1,817: 1, 1,836: 1, 1,838: 1, 1,861: 0, 1,863: 1, 1,868: 1, 1,880: 1, 1,885: 1, 1,896: 1, 1,916: 1, 1,924: 0, 1,939: 1, 1,952: 1, 1,966: 0, 1,980: 1, 2,038: 1, 2,070: 1, 2,094: 0, 2,123: 1, 2,139: 0, 2,144: 1, 2,163: 0, 2,182: 1, 2,183: 1, 2,184: 1, 2,196: 1, 2,197: 1, 2,220: 1, 2,229: 1, 2,238: 1, 2,246: 1, 2,258: 1, 2,266: 1, 2,268: 1, 2,273: 1, 2,279: 1, 2,294: 1, 2,309: 1, 2,312: 1, 2,323: 0, 2,325: 1, 2,343: 1, 2,366: 1, 2,377: 1, 2,379: 0, 2,391: 1, 2,401: 0, 2,402: 1, 2,406: 1, 2,415: 1, 2,476: 1, 2,480: 1, 2,484: 0, 2,507: 0, 2,513: 1, 2,535: 1, 2,562: 0, 2,596: 1, 2,612: 1, 2,620: 1, 2,635: 1, 2,655: 1, 2,657: 1, 2,678: 1, 2,684: 1, 2,685: 0, 2,714: 1, 2,725: 1, 2,751: 1, 2,753: 1, 2,772: 1, 2,792: 1, 2,800: 1, 2,828: 1, 2,862: 1, 2,875: 0, 2,882: 1, 2,894: 1, 2,911: 1, 2,938: 1, 2,940: 1, 2,955: 0, 2,961: 1, 3,000: 1, 3,004: 1, 3,027: 0, 3,054: 1, 3,101: 1, 3,102: 1, 3,107: 1, 3,117: 1, 3,128: 1, 3,154: 1, 3,160: 1, 3,166: 1, 3,179: 1, 3,204: 1, 3,209: 1, 3,224: 1, 3,260: 1, 3,262: 1, 3,290: 1, 3,303: 0, 3,314: 1, 3,337: 0, 3,347: 2, 3,460: 1, 3,482: 0, 3,489: 1, 3,505: 0, 3,511: 0, 3,546: 0, 3,573: 1, 3,576: 1, 3,592: 0, 3,652: 0, 3,674: 0, 3,684: 1, 3,716: 0, 3,718: 1, 3,787: 1, 3,860: 1, 3,894: 0, 3,897: 1, 3,899: 1, 3,905: 0, 3,948: 1, 3,953: 1, 4,031: 1, 4,043: 0, 4,077: 1, 4,078: 1, 4,084: 1, 4,096: 1, 4,119: 0, 4,129: 1, 4,173: 1, 4,187: 1, 4,195: 1, 4,199: 1, 4,305: 1, 4,308: 1, 4,317: 1, 4,318: 1, 4,337: 1, 4,350: 1, 4,353: 1, 4,563: 0, 4,746: 1, 4,873: 1, 4,909: 1, 4,963: 1, 4,969: 0, 4,999: 0, 5,107: 1, 5,228: 1, 5,307: 0, 5,319: 1, 5,414: 1, 5,427: 1, 5,551: 0, 5,559: 1, 5,759: 0, 5,783: 1, 5,810: 1, 5,815: 1, 5,828: 1, 5,830: 0, 5,840: 1, 5,874: 1, 5,941: 1, 5,945: 0, 5,946: 1, 6,012: 0, 6,136: 1, 6,202: 0, 6,209: 1, 6,254: 1, 6,352: 0, 6,379: 0, 6,425: 1, 6,443: 1, 6,505: 1, 6,642: 1, 6,643: 1, 6,696: 1, 6,715: 1, 6,738: 1, 6,834: 1, 6,869: 2, 6,908: 1, 6,960: 1, 6,991: 1, 7,016: 1, 7,067: 0, 7,095: 1, 7,115: 1, 7,212: 1, 7,290: 1, 7,424: 1, 7,484: 1, 7,634: 1, 7,675: 1, 7,745: 0, 7,805: 1, 7,890: 0, 8,022: 1, 8,158: 1, 8,177: 1, 8,265: 0, 8,363: 1, 8,413: 0, 8,517: 0, 8,541: 1, 8,615: 0, 8,759: 0, 8,921: 1, 8,971: 0, 9,018: 1, 9,202: 1, 9,805: 1, 9,808: 1, 10,272: 1, 10,329: 1, 10,453: 1, 10,544: 0, 10,619: 0, 10,754: 1, 10,758: 1, 10,991: 0, 11,395: 1, 11,500: 0, 11,978: 0, 12,334: 1, 12,362: 0, 12,444: 1, 12,843: 0, 13,009: 1, 13,054: 1, 13,403: 1, 13,677: 1, 13,697: 1, 13,732: 1, 13,916: 1, 14,231: 2, 14,716: 1, 14,849: 1, 15,063: 0, 15,129: 1, 15,161: 1, 15,236: 1, 15,313: 1, 15,343: 1, 15,454: 0, 15,511: 1, 15,699: 1, 15,767: 1, 15,889: 0, 15,905: 0, 16,363: 1, 16,645: 1, 16,767: 0, 16,962: 1, 17,631: 1, 18,877: 0, 19,296: 0, 19,551: 0, 20,546: 1, 20,745: 1, 21,364: 0, 21,437: 0, 22,295: 1, 30,979: 1, 33,075: 1, 33,624: 1, 35,237: 0, 35,447: 1, 35,755: 1, 36,249: 0, 37,860: 0, 38,714: 1, 43,225: 0, 45,044: 1

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels 0: 0

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs 0: 155

Sig_18_Blood.deconflicted_germline 48: 0, 148: 0, 193: 0, 226: 1, 434: 1, 466: 0, 469: 1, 506: 0, 701: 0, 755: 1, 765: 0, 786: 1, 830: 1, 1,122: 1, 1,133: 1, 1,139: 0, 1,206: 1, 1,216: 1, 1,266: 1, 1,298: 1, 1,312: 1, 1,315: 0, 1,316: 1, 1,372: 1, 1,404: 1, 1,430: 1, 1,437: 1, 1,560: 1, 1,585: 1, 1,588: 1, 1,599: 1, 1,610: 1, 1,632: 0, 1,640: 1, 1,675: 1, 1,676: 1, 1,695: 0, 1,696: 1, 1,728: 0, 1,750: 1, 1,790: 1, 1,802: 1, 1,803: 0, 1,827: 0, 1,847: 1, 1,867: 0, 1,872: 0, 1,925: 1, 1,931: 0, 1,945: 1, 1,948: 0, 1,959: 1, 1,961: 1, 1,965: 1, 1,973: 1, 1,978: 0, 2,050: 0, 2,053: 1, 2,074: 1, 2,076: 1, 2,097: 0, 2,109: 1, 2,148: 0, 2,152: 1, 2,179: 1, 2,190: 1, 2,234: 1, 2,252: 0, 2,290: 0, 2,310: 1, 2,322: 1, 2,332: 0, 2,335: 0, 2,336: 1, 2,367: 1, 2,415: 1, 2,422: 1, 2,427: 1, 2,460: 1, 2,472: 1, 2,490: 1, 2,495: 1, 2,499: 1, 2,518: 1, 2,540: 1, 2,557: 1, 2,572: 0, 2,594: 0, 2,606: 1, 2,612: 1, 2,641: 1, 2,654: 1, 2,664: 0, 2,697: 0, 2,725: 0, 2,735: 0, 2,745: 1, 2,771: 1, 2,776: 1, 2,816: 1, 2,828: 0, 2,832: 1, 2,848: 1, 2,885: 1, 2,907: 1, 2,963: 0, 2,986: 1, 2,990: 1, 3,003: 1, 3,004: 1, 3,010: 1, 3,063: 1, 3,071: 1, 3,123: 0, 3,138: 1, 3,151: 1, 3,177: 1, 3,243: 1, 3,322: 1, 3,328: 1, 3,355: 1, 3,375: 0, 3,389: 1, 3,404: 1, 3,431: 1, 3,449: 0, 3,451: 1, 3,457: 1, 3,465: 1, 3,466: 1, 3,509: 0, 3,534: 0, 3,537: 1, 3,542: 1, 3,543: 1, 3,586: 0, 3,619: 1, 3,627: 0, 3,632: 1, 3,653: 1, 3,658: 1, 3,667: 1, 3,674: 1, 3,738: 1, 3,801: 0, 3,823: 1, 3,851: 0, 3,872: 2, 3,891: 1, 3,907: 1, 3,911: 1, 3,941: 0, 3,942: 1, 3,949: 0, 4,020: 1, 4,056: 1, 4,083: 1, 4,102: 1, 4,123: 1, 4,168: 1, 4,208: 1, 4,310: 1, 4,316: 1, 4,366: 0, 4,373: 1, 4,384: 0, 4,420: 1, 4,440: 1, 4,474: 1, 4,594: 1, 4,655: 1, 4,659: 0, 4,727: 1, 4,747: 1, 4,761: 1, 4,787: 1, 4,804: 1, 4,806: 1, 4,836: 1, 4,838: 1, 4,880: 0, 4,914: 0, 4,921: 0, 4,979: 1, 5,008: 0, 5,038: 1, 5,040: 1, 5,048: 1, 5,099: 1, 5,144: 1, 5,205: 1, 5,218: 1, 5,219: 0, 5,303: 1, 5,321: 0, 5,377: 0, 5,398: 1, 5,405: 1, 5,484: 1, 5,515: 0, 5,586: 0, 5,606: 1, 5,649: 1, 5,716: 0, 5,750: 1, 5,763: 1, 5,829: 1, 5,831: 1, 5,858: 0, 5,902: 2, 5,917: 0, 5,986: 1, 5,991: 0, 6,012: 1, 6,090: 1, 6,104: 1, 6,173: 1, 6,292: 1, 6,424: 0, 6,527: 1, 6,563: 1, 6,578: 1, 6,637: 1, 6,687: 1, 6,737: 0, 6,750: 1, 6,785: 1, 6,808: 1, 6,846: 0, 6,888: 1, 6,989: 0, 7,029: 1, 7,159: 1, 7,195: 1, 7,197: 0, 7,214: 1, 7,608: 1, 7,612: 1, 7,636: 0, 7,657: 1, 7,724: 1, 7,729: 1, 7,743: 0, 7,756: 1, 7,758: 0, 7,765: 1, 7,824: 1, 7,896: 0, 7,897: 1, 7,907: 1, 8,005: 1, 8,039: 0, 8,156: 1, 8,196: 1, 8,206: 1, 8,275: 0, 8,297: 1, 8,364: 0, 8,377: 1, 8,399: 1, 8,512: 1, 8,709: 0, 8,728: 1, 8,814: 1, 8,868: 1, 8,886: 1, 8,974: 1, 8,986: 1, 8,995: 1, 9,003: 1, 9,077: 1, 9,080: 1, 9,100: 1, 9,200: 0, 9,252: 1, 9,295: 1, 9,360: 1, 9,428: 1, 9,430: 0, 9,471: 0, 9,510: 0, 9,801: 0, 9,836: 0, 9,845: 1, 9,953: 0, 10,214: 1, 10,217: 0, 10,623: 1, 10,647: 1, 10,995: 1, 11,041: 1, 11,043: 0, 11,092: 0, 11,122: 1, 11,156: 1, 11,159: 1, 11,238: 0, 11,257: 1, 11,414: 1, 11,497: 1, 11,533: 0, 11,985: 1, 12,051: 0, 12,251: 1, 12,503: 0, 12,650: 1, 12,966: 1, 13,107: 0, 13,255: 1, 13,677: 1, 13,923: 0, 13,973: 0, 14,298: 1, 14,493: 1, 14,736: 1, 14,969: 1, 15,013: 1, 15,113: 1, 15,211: 0, 15,684: 1, 16,265: 1, 16,890: 2, 17,730: 0, 19,079: 1, 19,367: 1, 19,595: 1, 19,613: 1, 19,671: 1, 19,746: 1, 19,971: 1, 20,129: 1, 20,369: 0, 20,855: 0, 22,259: 0, 22,325: 0, 22,363: 1, 22,626: 1, 22,949: 1, 23,288: 0, 23,430: 0, 23,529: 1, 23,723: 1, 24,057: 1, 24,189: 0, 24,211: 1, 24,213: 1, 24,219: 0, 24,360: 1, 24,369: 1, 24,434: 0, 24,544: 1, 24,813: 1, 24,959: 1, 25,128: 1, 25,441: 1, 25,851: 1, 26,200: 0, 26,356: 1, 26,651: 0, 27,416: 0, 28,524: 0, 29,524: 1, 29,881: 1, 29,979: 1, 32,909: 1, 33,061: 1, 33,639: 0, 33,937: 1, 34,068: 1, 34,327: 1, 35,795: 0, 36,258: 0, 37,203: 1, 47,750: 0, 47,881: 1, 52,465: 1, 53,967: 1, 54,929: 1, 55,182: 0, 56,417: 1, 56,907: 1, 61,334: 1, 61,722: 0, 64,325: 0, 71,282: 1, 73,423: 0, 75,216: 0, 78,636: 0

custom_Sig_18_tumor_normal.manta.diploid_sv 597: 0, 999: 0

custom_Sig_18_tumor_normal.strelka.somatic_indels 0: 0

custom_Sig_18_tumor_normal.strelka.somatic_snvs 0: 131


### Count Transversions

Samples: HCC1395_BL.deconflicted_germline, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs, Sig_18_Blood.deconflicted_germline, custom_Sig_18_tumor_normal.manta.diploid_sv, custom_Sig_18_tumor_normal.strelka.somatic_indels, custom_Sig_18_tumor_normal.strelka.somatic_snvs

HCC1395_BL.deconflicted_germline 67: 0, 136: 0, 256: 0, 497: 1, 627: 0, 645: 0, 695: 0, 712: 0, 747: 0, 790: 0, 796: 1, 813: 1, 946: 0, 1,021: 1, 1,057: 0, 1,078: 0, 1,096: 1, 1,159: 0, 1,177: 0, 1,188: 0, 1,189: 0, 1,209: 0, 1,216: 0, 1,221: 1, 1,293: 0, 1,334: 0, 1,362: 1, 1,369: 0, 1,370: 0, 1,371: 0, 1,390: 0, 1,396: 0, 1,399: 0, 1,400: 1, 1,402: 0, 1,446: 0, 1,457: 0, 1,461: 0, 1,474: 0, 1,480: 0, 1,522: 0, 1,547: 0, 1,551: 0, 1,553: 1, 1,576: 1, 1,591: 0, 1,593: 1, 1,624: 0, 1,639: 0, 1,656: 0, 1,667: 0, 1,669: 0, 1,676: 0, 1,677: 0, 1,680: 0, 1,697: 0, 1,699: 0, 1,725: 0, 1,729: 1, 1,730: 0, 1,764: 1, 1,791: 1, 1,816: 0, 1,817: 0, 1,836: 0, 1,838: 0, 1,861: 0, 1,863: 0, 1,868: 0, 1,880: 0, 1,885: 0, 1,896: 0, 1,916: 0, 1,924: 1, 1,939: 0, 1,952: 0, 1,966: 1, 1,980: 0, 2,038: 0, 2,070: 0, 2,094: 1, 2,123: 0, 2,139: 1, 2,144: 0, 2,163: 1, 2,182: 0, 2,183: 0, 2,184: 0, 2,196: 0, 2,197: 0, 2,220: 0, 2,229: 0, 2,238: 0, 2,246: 0, 2,258: 0, 2,266: 0, 2,268: 0, 2,273: 0, 2,279: 0, 2,294: 0, 2,309: 0, 2,312: 0, 2,323: 1, 2,325: 0, 2,343: 0, 2,366: 0, 2,377: 0, 2,379: 1, 2,391: 0, 2,401: 1, 2,402: 0, 2,406: 0, 2,415: 0, 2,476: 0, 2,480: 0, 2,484: 1, 2,507: 0, 2,513: 0, 2,535: 0, 2,562: 1, 2,596: 0, 2,612: 0, 2,620: 0, 2,635: 0, 2,655: 0, 2,657: 0, 2,678: 0, 2,684: 0, 2,685: 1, 2,714: 0, 2,725: 0, 2,751: 0, 2,753: 0, 2,772: 0, 2,792: 0, 2,800: 0, 2,828: 0, 2,862: 0, 2,875: 1, 2,882: 0, 2,894: 0, 2,911: 0, 2,938: 0, 2,940: 0, 2,955: 1, 2,961: 0, 3,000: 0, 3,004: 0, 3,027: 1, 3,054: 0, 3,101: 0, 3,102: 0, 3,107: 0, 3,117: 0, 3,128: 0, 3,154: 0, 3,160: 0, 3,166: 0, 3,179: 0, 3,204: 0, 3,209: 0, 3,224: 0, 3,260: 0, 3,262: 0, 3,290: 0, 3,303: 0, 3,314: 0, 3,337: 1, 3,347: 0, 3,460: 0, 3,482: 1, 3,489: 0, 3,505: 1, 3,511: 1, 3,546: 1, 3,573: 0, 3,576: 0, 3,592: 1, 3,652: 1, 3,674: 1, 3,684: 0, 3,716: 1, 3,718: 0, 3,787: 0, 3,860: 0, 3,894: 1, 3,897: 0, 3,899: 0, 3,905: 1, 3,948: 0, 3,953: 0, 4,031: 0, 4,043: 1, 4,077: 0, 4,078: 0, 4,084: 0, 4,096: 0, 4,119: 1, 4,129: 0, 4,173: 0, 4,187: 0, 4,195: 0, 4,199: 0, 4,305: 0, 4,308: 0, 4,317: 0, 4,318: 0, 4,337: 0, 4,350: 0, 4,353: 0, 4,563: 0, 4,746: 0, 4,873: 0, 4,909: 0, 4,963: 0, 4,969: 0, 4,999: 1, 5,107: 1, 5,228: 0, 5,307: 1, 5,319: 0, 5,414: 0, 5,427: 0, 5,551: 0, 5,559: 0, 5,759: 0, 5,783: 0, 5,810: 0, 5,815: 0, 5,828: 0, 5,830: 1, 5,840: 0, 5,874: 0, 5,941: 0, 5,945: 1, 5,946: 0, 6,012: 0, 6,136: 0, 6,202: 1, 6,209: 0, 6,254: 0, 6,352: 0, 6,379: 1, 6,425: 0, 6,443: 0, 6,505: 0, 6,642: 0, 6,643: 0, 6,696: 0, 6,715: 0, 6,738: 0, 6,834: 0, 6,869: 0, 6,908: 0, 6,960: 0, 6,991: 0, 7,016: 0, 7,067: 1, 7,095: 0, 7,115: 0, 7,212: 0, 7,290: 0, 7,424: 0, 7,484: 0, 7,634: 0, 7,675: 0, 7,745: 1, 7,805: 0, 7,890: 1, 8,022: 0, 8,158: 0, 8,177: 0, 8,265: 1, 8,363: 0, 8,413: 1, 8,517: 0, 8,541: 0, 8,615: 1, 8,759: 1, 8,921: 0, 8,971: 1, 9,018: 0, 9,202: 0, 9,805: 0, 9,808: 0, 10,272: 0, 10,329: 0, 10,453: 0, 10,544: 1, 10,619: 1, 10,754: 0, 10,758: 0, 10,991: 1, 11,395: 0, 11,500: 0, 11,978: 0, 12,334: 0, 12,362: 1, 12,444: 0, 12,843: 1, 13,009: 0, 13,054: 0, 13,403: 0, 13,677: 0, 13,697: 0, 13,732: 0, 13,916: 0, 14,231: 0, 14,716: 0, 14,849: 0, 15,063: 1, 15,129: 0, 15,161: 0, 15,236: 0, 15,313: 0, 15,343: 0, 15,454: 1, 15,511: 0, 15,699: 0, 15,767: 0, 15,889: 1, 15,905: 1, 16,363: 0, 16,645: 0, 16,767: 1, 16,962: 1, 17,631: 0, 18,877: 0, 19,296: 1, 19,551: 1, 20,546: 0, 20,745: 0, 21,364: 0, 21,437: 0, 22,295: 0, 30,979: 0, 33,075: 0, 33,624: 0, 35,237: 1, 35,447: 0, 35,755: 0, 36,249: 1, 37,860: 1, 38,714: 0, 43,225: 1, 45,044: 0

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels 0: 0

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs 0: 145

Sig_18_Blood.deconflicted_germline 48: 1, 148: 0, 193: 0, 226: 0, 434: 0, 466: 1, 469: 0, 506: 1, 701: 1, 755: 0, 765: 0, 786: 0, 830: 0, 1,122: 0, 1,133: 0, 1,139: 1, 1,206: 0, 1,216: 0, 1,266: 0, 1,298: 0, 1,312: 0, 1,315: 1, 1,316: 0, 1,372: 0, 1,404: 0, 1,430: 0, 1,437: 0, 1,560: 0, 1,585: 0, 1,588: 0, 1,599: 0, 1,610: 0, 1,632: 1, 1,640: 0, 1,675: 0, 1,676: 0, 1,695: 0, 1,696: 0, 1,728: 1, 1,750: 0, 1,790: 0, 1,802: 0, 1,803: 1, 1,827: 0, 1,847: 0, 1,867: 1, 1,872: 0, 1,925: 0, 1,931: 1, 1,945: 0, 1,948: 1, 1,959: 0, 1,961: 0, 1,965: 0, 1,973: 0, 1,978: 1, 2,050: 0, 2,053: 0, 2,074: 0, 2,076: 0, 2,097: 0, 2,109: 0, 2,148: 1, 2,152: 0, 2,179: 0, 2,190: 0, 2,234: 0, 2,252: 1, 2,290: 0, 2,310: 0, 2,322: 0, 2,332: 1, 2,335: 0, 2,336: 0, 2,367: 0, 2,415: 0, 2,422: 0, 2,427: 0, 2,460: 0, 2,472: 0, 2,490: 0, 2,495: 0, 2,499: 0, 2,518: 0, 2,540: 1, 2,557: 0, 2,572: 1, 2,594: 1, 2,606: 0, 2,612: 0, 2,641: 0, 2,654: 0, 2,664: 1, 2,697: 1, 2,725: 1, 2,735: 1, 2,745: 0, 2,771: 0, 2,776: 0, 2,816: 0, 2,828: 0, 2,832: 0, 2,848: 0, 2,885: 0, 2,907: 0, 2,963: 1, 2,986: 0, 2,990: 0, 3,003: 0, 3,004: 0, 3,010: 0, 3,063: 0, 3,071: 0, 3,123: 1, 3,138: 0, 3,151: 0, 3,177: 0, 3,243: 0, 3,322: 0, 3,328: 0, 3,355: 0, 3,375: 1, 3,389: 0, 3,404: 0, 3,431: 0, 3,449: 1, 3,451: 0, 3,457: 0, 3,465: 0, 3,466: 0, 3,509: 1, 3,534: 1, 3,537: 0, 3,542: 0, 3,543: 0, 3,586: 1, 3,619: 0, 3,627: 1, 3,632: 0, 3,653: 0, 3,658: 0, 3,667: 0, 3,674: 0, 3,738: 0, 3,801: 1, 3,823: 0, 3,851: 1, 3,872: 0, 3,891: 0, 3,907: 0, 3,911: 0, 3,941: 0, 3,942: 0, 3,949: 1, 4,020: 0, 4,056: 0, 4,083: 0, 4,102: 0, 4,123: 0, 4,168: 0, 4,208: 0, 4,310: 0, 4,316: 0, 4,366: 1, 4,373: 0, 4,384: 1, 4,420: 0, 4,440: 0, 4,474: 0, 4,594: 0, 4,655: 0, 4,659: 1, 4,727: 0, 4,747: 0, 4,761: 0, 4,787: 0, 4,804: 0, 4,806: 0, 4,836: 0, 4,838: 0, 4,880: 1, 4,914: 1, 4,921: 1, 4,979: 0, 5,008: 1, 5,038: 0, 5,040: 0, 5,048: 0, 5,099: 0, 5,144: 0, 5,205: 0, 5,218: 0, 5,219: 1, 5,303: 0, 5,321: 1, 5,377: 1, 5,398: 0, 5,405: 0, 5,484: 0, 5,515: 1, 5,586: 1, 5,606: 0, 5,649: 0, 5,716: 1, 5,750: 0, 5,763: 0, 5,829: 0, 5,831: 0, 5,858: 1, 5,902: 0, 5,917: 1, 5,986: 0, 5,991: 1, 6,012: 0, 6,090: 0, 6,104: 0, 6,173: 0, 6,292: 0, 6,424: 1, 6,527: 0, 6,563: 0, 6,578: 0, 6,637: 1, 6,687: 0, 6,737: 1, 6,750: 0, 6,785: 0, 6,808: 0, 6,846: 1, 6,888: 0, 6,989: 1, 7,029: 0, 7,159: 0, 7,195: 0, 7,197: 1, 7,214: 0, 7,608: 0, 7,612: 0, 7,636: 0, 7,657: 0, 7,724: 0, 7,729: 0, 7,743: 1, 7,756: 0, 7,758: 1, 7,765: 0, 7,824: 0, 7,896: 1, 7,897: 0, 7,907: 0, 8,005: 0, 8,039: 1, 8,156: 0, 8,196: 0, 8,206: 0, 8,275: 0, 8,297: 0, 8,364: 0, 8,377: 0, 8,399: 0, 8,512: 0, 8,709: 0, 8,728: 0, 8,814: 0, 8,868: 0, 8,886: 0, 8,974: 0, 8,986: 0, 8,995: 0, 9,003: 0, 9,077: 0, 9,080: 0, 9,100: 0, 9,200: 1, 9,252: 0, 9,295: 0, 9,360: 1, 9,428: 0, 9,430: 1, 9,471: 1, 9,510: 1, 9,801: 1, 9,836: 1, 9,845: 0, 9,953: 0, 10,214: 0, 10,217: 1, 10,623: 0, 10,647: 0, 10,995: 0, 11,041: 0, 11,043: 1, 11,092: 1, 11,122: 0, 11,156: 0, 11,159: 0, 11,238: 1, 11,257: 0, 11,414: 0, 11,497: 0, 11,533: 1, 11,985: 0, 12,051: 1, 12,251: 0, 12,503: 1, 12,650: 0, 12,966: 0, 13,107: 0, 13,255: 0, 13,677: 0, 13,923: 1, 13,973: 1, 14,298: 0, 14,493: 0, 14,736: 0, 14,969: 0, 15,013: 0, 15,113: 0, 15,211: 1, 15,684: 0, 16,265: 0, 16,890: 0, 17,730: 0, 19,079: 0, 19,367: 0, 19,595: 0, 19,613: 0, 19,671: 0, 19,746: 0, 19,971: 0, 20,129: 0, 20,369: 1, 20,855: 1, 22,259: 1, 22,325: 1, 22,363: 0, 22,626: 0, 22,949: 0, 23,288: 0, 23,430: 1, 23,529: 0, 23,723: 0, 24,057: 0, 24,189: 1, 24,211: 0, 24,213: 0, 24,219: 1, 24,360: 0, 24,369: 0, 24,434: 1, 24,544: 0, 24,813: 0, 24,959: 0, 25,128: 0, 25,441: 0, 25,851: 0, 26,200: 0, 26,356: 0, 26,651: 1, 27,416: 1, 28,524: 0, 29,524: 0, 29,881: 0, 29,979: 0, 32,909: 0, 33,061: 0, 33,639: 0, 33,937: 0, 34,068: 0, 34,327: 0, 35,795: 0, 36,258: 1, 37,203: 0, 47,750: 1, 47,881: 0, 52,465: 0, 53,967: 0, 54,929: 0, 55,182: 1, 56,417: 0, 56,907: 0, 61,334: 0, 61,722: 1, 64,325: 1, 71,282: 0, 73,423: 1, 75,216: 1, 78,636: 0

custom_Sig_18_tumor_normal.manta.diploid_sv 597: 0, 999: 0

custom_Sig_18_tumor_normal.strelka.somatic_indels 0: 0

custom_Sig_18_tumor_normal.strelka.somatic_snvs 0: 106


### Count Indels

Samples: HCC1395_BL.deconflicted_germline, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs, Sig_18_Blood.deconflicted_germline, custom_Sig_18_tumor_normal.manta.diploid_sv, custom_Sig_18_tumor_normal.strelka.somatic_indels, custom_Sig_18_tumor_normal.strelka.somatic_snvs

HCC1395_BL.deconflicted_germline 67: 0, 136: 0, 256: 0, 497: 0, 627: 0, 645: 0, 695: 0, 712: 0, 747: 0, 790: 0, 796: 0, 813: 0, 946: 0, 1,021: 0, 1,057: 0, 1,078: 0, 1,096: 0, 1,159: 0, 1,177: 0, 1,188: 0, 1,189: 0, 1,209: 0, 1,216: 0, 1,221: 0, 1,293: 0, 1,334: 0, 1,362: 0, 1,369: 0, 1,370: 0, 1,371: 0, 1,390: 0, 1,396: 0, 1,399: 0, 1,400: 0, 1,402: 0, 1,446: 0, 1,457: 0, 1,461: 0, 1,474: 1, 1,480: 1, 1,522: 0, 1,547: 1, 1,551: 0, 1,553: 0, 1,576: 0, 1,591: 0, 1,593: 0, 1,624: 0, 1,639: 0, 1,656: 0, 1,667: 0, 1,669: 0, 1,676: 0, 1,677: 0, 1,680: 0, 1,697: 0, 1,699: 0, 1,725: 0, 1,729: 0, 1,730: 0, 1,764: 0, 1,791: 0, 1,816: 0, 1,817: 0, 1,836: 0, 1,838: 0, 1,861: 1, 1,863: 0, 1,868: 0, 1,880: 0, 1,885: 0, 1,896: 0, 1,916: 0, 1,924: 0, 1,939: 0, 1,952: 0, 1,966: 0, 1,980: 0, 2,038: 0, 2,070: 0, 2,094: 0, 2,123: 0, 2,139: 0, 2,144: 0, 2,163: 0, 2,182: 0, 2,183: 0, 2,184: 0, 2,196: 0, 2,197: 0, 2,220: 0, 2,229: 0, 2,238: 0, 2,246: 0, 2,258: 0, 2,266: 0, 2,268: 0, 2,273: 0, 2,279: 0, 2,294: 0, 2,309: 0, 2,312: 0, 2,323: 0, 2,325: 0, 2,343: 0, 2,366: 0, 2,377: 0, 2,379: 0, 2,391: 0, 2,401: 0, 2,402: 0, 2,406: 0, 2,415: 0, 2,476: 0, 2,480: 0, 2,484: 0, 2,507: 1, 2,513: 0, 2,535: 0, 2,562: 0, 2,596: 0, 2,612: 0, 2,620: 0, 2,635: 0, 2,655: 0, 2,657: 0, 2,678: 0, 2,684: 0, 2,685: 0, 2,714: 0, 2,725: 0, 2,751: 0, 2,753: 0, 2,772: 0, 2,792: 0, 2,800: 0, 2,828: 0, 2,862: 0, 2,875: 0, 2,882: 0, 2,894: 0, 2,911: 0, 2,938: 0, 2,940: 0, 2,955: 0, 2,961: 0, 3,000: 0, 3,004: 0, 3,027: 0, 3,054: 0, 3,101: 0, 3,102: 0, 3,107: 0, 3,117: 0, 3,128: 0, 3,154: 0, 3,160: 0, 3,166: 0, 3,179: 0, 3,204: 0, 3,209: 0, 3,224: 0, 3,260: 0, 3,262: 0, 3,290: 0, 3,303: 1, 3,314: 0, 3,337: 0, 3,347: 0, 3,460: 0, 3,482: 0, 3,489: 0, 3,505: 0, 3,511: 0, 3,546: 0, 3,573: 0, 3,576: 0, 3,592: 0, 3,652: 0, 3,674: 0, 3,684: 0, 3,716: 0, 3,718: 0, 3,787: 0, 3,860: 0, 3,894: 0, 3,897: 0, 3,899: 0, 3,905: 0, 3,948: 0, 3,953: 0, 4,031: 0, 4,043: 0, 4,077: 0, 4,078: 0, 4,084: 0, 4,096: 0, 4,119: 0, 4,129: 0, 4,173: 0, 4,187: 0, 4,195: 0, 4,199: 0, 4,305: 0, 4,308: 0, 4,317: 0, 4,318: 0, 4,337: 0, 4,350: 0, 4,353: 0, 4,563: 1, 4,746: 0, 4,873: 0, 4,909: 0, 4,963: 0, 4,969: 1, 4,999: 0, 5,107: 0, 5,228: 0, 5,307: 0, 5,319: 0, 5,414: 0, 5,427: 0, 5,551: 1, 5,559: 0, 5,759: 2, 5,783: 0, 5,810: 0, 5,815: 0, 5,828: 0, 5,830: 0, 5,840: 0, 5,874: 0, 5,941: 0, 5,945: 0, 5,946: 0, 6,012: 1, 6,136: 0, 6,202: 0, 6,209: 0, 6,254: 0, 6,352: 1, 6,379: 0, 6,425: 0, 6,443: 0, 6,505: 0, 6,642: 0, 6,643: 0, 6,696: 0, 6,715: 0, 6,738: 0, 6,834: 0, 6,869: 0, 6,908: 0, 6,960: 0, 6,991: 0, 7,016: 0, 7,067: 0, 7,095: 0, 7,115: 0, 7,212: 0, 7,290: 0, 7,424: 0, 7,484: 0, 7,634: 0, 7,675: 0, 7,745: 0, 7,805: 0, 7,890: 0, 8,022: 0, 8,158: 0, 8,177: 0, 8,265: 0, 8,363: 0, 8,413: 0, 8,517: 1, 8,541: 0, 8,615: 0, 8,759: 0, 8,921: 0, 8,971: 0, 9,018: 0, 9,202: 0, 9,805: 0, 9,808: 0, 10,272: 0, 10,329: 0, 10,453: 0, 10,544: 0, 10,619: 0, 10,754: 0, 10,758: 0, 10,991: 0, 11,395: 0, 11,500: 1, 11,978: 2, 12,334: 0, 12,362: 0, 12,444: 0, 12,843: 0, 13,009: 0, 13,054: 0, 13,403: 0, 13,677: 0, 13,697: 0, 13,732: 0, 13,916: 0, 14,231: 0, 14,716: 0, 14,849: 0, 15,063: 0, 15,129: 0, 15,161: 0, 15,236: 0, 15,313: 0, 15,343: 0, 15,454: 0, 15,511: 0, 15,699: 0, 15,767: 0, 15,889: 0, 15,905: 0, 16,363: 0, 16,645: 0, 16,767: 0, 16,962: 0, 17,631: 0, 18,877: 1, 19,296: 0, 19,551: 0, 20,546: 0, 20,745: 0, 21,364: 1, 21,437: 1, 22,295: 0, 30,979: 0, 33,075: 0, 33,624: 0, 35,237: 0, 35,447: 0, 35,755: 0, 36,249: 0, 37,860: 0, 38,714: 0, 43,225: 0, 45,044: 0

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels 0: 42

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs 0: 0

Sig_18_Blood.deconflicted_germline 48: 0, 148: 1, 193: 1, 226: 0, 434: 0, 466: 0, 469: 0, 506: 0, 701: 0, 755: 0, 765: 1, 786: 0, 830: 0, 1,122: 0, 1,133: 0, 1,139: 0, 1,206: 0, 1,216: 0, 1,266: 0, 1,298: 0, 1,312: 0, 1,315: 0, 1,316: 0, 1,372: 0, 1,404: 0, 1,430: 0, 1,437: 0, 1,560: 0, 1,585: 0, 1,588: 0, 1,599: 0, 1,610: 0, 1,632: 0, 1,640: 0, 1,675: 0, 1,676: 0, 1,695: 1, 1,696: 0, 1,728: 0, 1,750: 0, 1,790: 0, 1,802: 0, 1,803: 0, 1,827: 1, 1,847: 0, 1,867: 0, 1,872: 1, 1,925: 0, 1,931: 0, 1,945: 0, 1,948: 0, 1,959: 0, 1,961: 0, 1,965: 0, 1,973: 0, 1,978: 0, 2,050: 1, 2,053: 0, 2,074: 0, 2,076: 0, 2,097: 1, 2,109: 0, 2,148: 0, 2,152: 0, 2,179: 0, 2,190: 0, 2,234: 0, 2,252: 0, 2,290: 1, 2,310: 0, 2,322: 0, 2,332: 0, 2,335: 1, 2,336: 0, 2,367: 0, 2,415: 0, 2,422: 0, 2,427: 0, 2,460: 0, 2,472: 0, 2,490: 0, 2,495: 0, 2,499: 0, 2,518: 0, 2,540: 0, 2,557: 0, 2,572: 0, 2,594: 0, 2,606: 0, 2,612: 0, 2,641: 0, 2,654: 0, 2,664: 0, 2,697: 0, 2,725: 0, 2,735: 0, 2,745: 0, 2,771: 0, 2,776: 0, 2,816: 0, 2,828: 1, 2,832: 0, 2,848: 0, 2,885: 0, 2,907: 0, 2,963: 0, 2,986: 0, 2,990: 0, 3,003: 0, 3,004: 0, 3,010: 0, 3,063: 0, 3,071: 0, 3,123: 0, 3,138: 0, 3,151: 0, 3,177: 0, 3,243: 0, 3,322: 0, 3,328: 0, 3,355: 0, 3,375: 0, 3,389: 0, 3,404: 0, 3,431: 0, 3,449: 0, 3,451: 0, 3,457: 0, 3,465: 0, 3,466: 0, 3,509: 0, 3,534: 0, 3,537: 0, 3,542: 0, 3,543: 0, 3,586: 0, 3,619: 0, 3,627: 0, 3,632: 0, 3,653: 0, 3,658: 0, 3,667: 0, 3,674: 0, 3,738: 0, 3,801: 0, 3,823: 0, 3,851: 0, 3,872: 0, 3,891: 0, 3,907: 0, 3,911: 0, 3,941: 1, 3,942: 0, 3,949: 0, 4,020: 0, 4,056: 0, 4,083: 0, 4,102: 0, 4,123: 0, 4,168: 0, 4,208: 0, 4,310: 0, 4,316: 0, 4,366: 0, 4,373: 0, 4,384: 0, 4,420: 0, 4,440: 0, 4,474: 0, 4,594: 0, 4,655: 0, 4,659: 0, 4,727: 0, 4,747: 0, 4,761: 0, 4,787: 0, 4,804: 0, 4,806: 0, 4,836: 0, 4,838: 0, 4,880: 0, 4,914: 0, 4,921: 0, 4,979: 0, 5,008: 0, 5,038: 0, 5,040: 0, 5,048: 0, 5,099: 0, 5,144: 0, 5,205: 0, 5,218: 0, 5,219: 0, 5,303: 0, 5,321: 0, 5,377: 0, 5,398: 0, 5,405: 0, 5,484: 0, 5,515: 0, 5,586: 0, 5,606: 0, 5,649: 0, 5,716: 0, 5,750: 0, 5,763: 0, 5,829: 0, 5,831: 0, 5,858: 0, 5,902: 0, 5,917: 0, 5,986: 0, 5,991: 0, 6,012: 0, 6,090: 0, 6,104: 0, 6,173: 0, 6,292: 0, 6,424: 0, 6,527: 0, 6,563: 0, 6,578: 0, 6,637: 0, 6,687: 0, 6,737: 0, 6,750: 0, 6,785: 0, 6,808: 0, 6,846: 0, 6,888: 0, 6,989: 0, 7,029: 0, 7,159: 0, 7,195: 0, 7,197: 0, 7,214: 0, 7,608: 0, 7,612: 0, 7,636: 2, 7,657: 0, 7,724: 0, 7,729: 0, 7,743: 0, 7,756: 0, 7,758: 0, 7,765: 0, 7,824: 0, 7,896: 0, 7,897: 0, 7,907: 0, 8,005: 0, 8,039: 0, 8,156: 0, 8,196: 0, 8,206: 0, 8,275: 1, 8,297: 0, 8,364: 1, 8,377: 0, 8,399: 0, 8,512: 0, 8,709: 1, 8,728: 0, 8,814: 0, 8,868: 0, 8,886: 0, 8,974: 0, 8,986: 0, 8,995: 0, 9,003: 0, 9,077: 0, 9,080: 0, 9,100: 0, 9,200: 0, 9,252: 0, 9,295: 0, 9,360: 0, 9,428: 0, 9,430: 0, 9,471: 0, 9,510: 0, 9,801: 0, 9,836: 0, 9,845: 0, 9,953: 1, 10,214: 0, 10,217: 0, 10,623: 0, 10,647: 0, 10,995: 0, 11,041: 0, 11,043: 0, 11,092: 0, 11,122: 0, 11,156: 0, 11,159: 0, 11,238: 0, 11,257: 0, 11,414: 0, 11,497: 0, 11,533: 0, 11,985: 0, 12,051: 0, 12,251: 0, 12,503: 0, 12,650: 0, 12,966: 0, 13,107: 1, 13,255: 0, 13,677: 0, 13,923: 0, 13,973: 0, 14,298: 0, 14,493: 0, 14,736: 0, 14,969: 0, 15,013: 0, 15,113: 0, 15,211: 0, 15,684: 0, 16,265: 0, 16,890: 0, 17,730: 1, 19,079: 0, 19,367: 0, 19,595: 0, 19,613: 0, 19,671: 0, 19,746: 0, 19,971: 0, 20,129: 0, 20,369: 0, 20,855: 0, 22,259: 0, 22,325: 0, 22,363: 0, 22,626: 0, 22,949: 0, 23,288: 1, 23,430: 0, 23,529: 0, 23,723: 0, 24,057: 0, 24,189: 0, 24,211: 0, 24,213: 0, 24,219: 0, 24,360: 0, 24,369: 0, 24,434: 0, 24,544: 0, 24,813: 0, 24,959: 0, 25,128: 0, 25,441: 0, 25,851: 0, 26,200: 1, 26,356: 0, 26,651: 0, 27,416: 0, 28,524: 1, 29,524: 0, 29,881: 0, 29,979: 0, 32,909: 0, 33,061: 0, 33,639: 1, 33,937: 0, 34,068: 0, 34,327: 0, 35,795: 1, 36,258: 0, 37,203: 0, 47,750: 0, 47,881: 0, 52,465: 0, 53,967: 0, 54,929: 0, 55,182: 0, 56,417: 0, 56,907: 0, 61,334: 0, 61,722: 0, 64,325: 0, 71,282: 0, 73,423: 0, 75,216: 0, 78,636: 1

custom_Sig_18_tumor_normal.manta.diploid_sv 597: 1, 999: 2

custom_Sig_18_tumor_normal.strelka.somatic_indels 0: 88

custom_Sig_18_tumor_normal.strelka.somatic_snvs 0: 0



----------------------

Tool: Bcftools
Section: Indel Distribution
Title: Bcftools Stats: Indel Distribution

Plot type: x/y line
X axis: InDel Length (bp)
Y axis: Count

Samples: HCC1395_BL, HCC1395_BL.deconflicted_germline, HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv, HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs, Sig_18_Blood, Sig_18_Blood.deconflicted_germline, custom_Sig_18_tumor_normal.manta.diploid_sv, custom_Sig_18_tumor_normal.manta.somatic_sv, custom_Sig_18_tumor_normal.strelka.somatic_indels, custom_Sig_18_tumor_normal.strelka.somatic_snvs

X values are in  bp

HCC1395_BL 0: N/A

HCC1395_BL.deconflicted_germline -15: 1, -9: 1, -6: 1, -4: 1, -2: 2, -1: 5, 0: N/A, 1: 4, 2: 2, 3: 2, 6: 1

HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv 0: N/A

HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv 0: N/A

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels -24: 1, -10: 1, -9: 2, -4: 2, -3: 5, -2: 2, -1: 10, 0: N/A, 1: 17, 3: 1, 4: 1

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs 0: N/A

Sig_18_Blood 0: N/A

Sig_18_Blood.deconflicted_germline -15: 1, -10: 1, -9: 1, -6: 1, -5: 1, -3: 1, -2: 2, -1: 6, 0: N/A, 1: 4, 2: 3, 3: 1, 5: 1, 6: 1, 39: 1, 40: 1

custom_Sig_18_tumor_normal.manta.diploid_sv -60: 2, 0: N/A, 57: 1

custom_Sig_18_tumor_normal.manta.somatic_sv 0: N/A

custom_Sig_18_tumor_normal.strelka.somatic_indels -8: 1, -4: 4, -3: 8, -2: 11, -1: 28, 0: N/A, 1: 33, 2: 1, 3: 2

custom_Sig_18_tumor_normal.strelka.somatic_snvs 0: N/A

----------------------

Tool: Bcftools
Section: Variant depths
Section description: Read depth support distribution for called variants
Title: Bcftools Stats: Variant depths

Plot type: x/y line
X axis: Variant depth
Y axis: Fraction of sites (%)

Samples: HCC1395_BL.deconflicted_germline, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs, Sig_18_Blood.deconflicted_germline, custom_Sig_18_tumor_normal.strelka.somatic_snvs

Y values are in %

HCC1395_BL.deconflicted_germline 3: 0, 7: 0, 9: 0, 28: 0, 30: 0, 43: 0, 45: 0, 47: 0, 48: 0, 52: 0, 57: 0, 59: 0, 60: 0, 63: 0, 65: 0, 66: 0, 68: 0, 74: 0, 75: 0, 77: 0, 78: 0, 81: 0, 83: 0, 84: 0, 85: 0, 87: 0, 88: 0, 89: 0, 92: 0, 93: 0, 94: 0, 95: 0, 97: 0, 98: 0, 101: 0, 102: 0, 104: 0, 106: 0, 107: 0, 109: 0, 110: 0, 112: 0, 113: 0, 114: 0, 115: 0, 116: 0, 117: 0, 118: 0, 119: 0, 120: 0, 121: 0, 122: 0, 123: 0, 124: 0, 125: 0, 126: 0, 127: 0, 128: 1, 129: 0, 130: 0, 131: 0, 132: 0, 133: 0, 134: 0, 135: 0, 136: 0, 137: 0, 138: 0, 139: 0, 140: 0, 142: 0, 143: 1, 144: 0, 145: 0, 146: 0, 147: 0, 148: 0, 149: 1, 150: 0, 151: 0, 152: 0, 153: 0, 155: 0, 156: 0, 157: 0, 158: 0, 159: 0, 160: 0, 161: 0, 162: 0, 163: 0, 164: 0, 165: 0, 166: 0, 167: 0, 168: 0, 169: 0, 170: 0, 171: 0, 172: 0, 173: 0, 174: 0, 175: 0, 176: 0, 177: 0, 178: 0, 179: 0, 180: 0, 181: 0, 182: 0, 183: 1, 184: 0, 185: 0, 186: 0, 187: 0, 188: 0, 189: 0, 190: 0, 191: 1, 192: 0, 193: 0, 194: 0, 195: 0, 196: 0, 197: 0, 198: 0, 199: 0, 200: 0, 201: 0, 202: 0, 203: 0, 204: 0, 205: 0, 206: 0, 207: 0, 208: 0, 209: 0, 210: 0, 211: 0, 212: 0, 213: 0, 214: 0, 215: 0, 216: 0, 217: 0, 218: 0, 219: 0, 220: 0, 221: 0, 222: 0, 223: 0, 224: 0, 225: 0, 226: 0, 227: 0, 228: 0, 229: 0, 230: 0, 231: 0, 232: 0, 233: 1, 234: 0, 235: 0, 236: 0, 237: 0, 238: 0, 239: 0, 240: 0, 241: 0, 242: 0, 243: 0, 244: 0, 245: 0, 246: 0, 247: 0, 248: 0, 249: 0, 250: 0, 251: 0, 252: 0, 253: 0, 254: 0, 255: 0, 256: 0, 257: 0, 258: 0, 259: 0, 260: 0, 261: 0, 262: 0, 263: 0, 264: 0, 265: 0, 266: 0, 267: 0, 268: 0, 269: 0, 270: 0, 271: 0, 272: 0, 273: 0, 274: 0, 275: 0, 276: 0, 277: 0, 278: 0, 279: 0, 280: 0, 281: 0, 282: 0, 283: 0, 284: 0, 285: 0, 286: 0, 288: 0, 289: 0, 290: 0, 291: 0, 292: 0, 293: 0, 294: 0, 295: 0, 296: 0, 298: 0, 299: 0, 300: 0, 301: 0, 302: 0, 303: 0, 304: 0, 306: 0, 307: 0, 309: 0, 311: 0, 312: 0, 313: 0, 314: 0, 315: 0, 316: 0, 317: 0, 318: 0, 320: 0, 321: 0, 322: 0, 323: 0, 325: 0, 326: 0, 327: 0, 328: 0, 330: 0, 331: 0, 332: 0, 333: 0, 334: 0, 336: 0, 337: 0, 338: 0, 339: 0, 340: 0, 341: 0, 342: 0, 343: 0, 344: 0, 345: 0, 346: 0, 348: 0, 349: 0, 351: 0, 353: 0, 354: 0, 355: 0, 356: 0, 358: 0, 359: 0, 360: 0, 362: 0, 363: 0, 364: 0, 365: 0, 366: 0, 367: 0, 368: 0, 369: 0, 370: 0, 371: 0, 372: 0, 373: 0, 374: 0, 375: 0, 377: 0, 378: 0, 379: 0, 380: 0, 381: 0, 382: 0, 383: 0, 385: 0, 386: 0, 387: 0, 388: 0, 390: 0, 391: 0, 392: 0, 393: 0, 395: 0, 397: 0, 398: 0, 399: 0, 400: 0, 402: 0, 405: 0, 408: 0, 409: 0, 413: 0, 414: 0, 415: 0, 416: 0, 417: 0, 418: 0, 419: 0, 421: 0, 422: 0, 425: 0, 426: 0, 427: 0, 428: 0, 429: 0, 430: 0, 432: 0, 433: 0, 434: 0, 439: 0, 440: 0, 441: 0, 442: 0, 447: 0, 448: 0, 449: 0, 450: 0, 452: 0, 453: 0, 454: 0, 456: 0, 458: 0, 459: 0, 460: 0, 462: 0, 463: 0, 464: 0, 465: 0, 466: 0, 467: 0, 469: 0, 472: 0, 473: 0, 474: 0, 475: 0, 477: 0, 478: 0, 479: 0, 480: 0, 481: 0, 482: 0, 483: 0, 484: 0, 485: 0, 486: 0, 487: 0, 490: 0, 491: 0, 492: 0, 493: 0, 494: 0, 496: 0, 497: 0, 499: 0, >500: 16, 500: 0

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs 3: 0, 7: 0, 9: 0, 28: 0, 30: 0, 43: 0, 45: 0, 47: 0, 48: 0, 52: 0, 57: 0, 59: 0, 60: 0, 63: 0, 65: 0, 66: 0, 68: 0, 74: 0, 75: 0, 77: 0, 78: 0, 81: 0, 83: 0, 84: 0, 85: 0, 87: 0, 88: 0, 89: 0, 92: 0, 93: 0, 94: 0, 95: 0, 97: 0, 98: 0, 101: 0, 102: 0, 104: 0, 106: 0, 107: 0, 109: 0, 110: 0, 112: 0, 113: 0, 114: 0, 115: 0, 116: 0, 117: 0, 118: 0, 119: 0, 120: 0, 121: 0, 122: 0, 123: 0, 124: 0, 125: 0, 126: 0, 127: 0, 128: 0, 129: 0, 130: 0, 131: 0, 132: 0, 133: 0, 134: 0, 135: 0, 136: 0, 137: 0, 138: 0, 139: 0, 140: 0, 142: 0, 143: 0, 144: 1, 145: 0, 146: 0, 147: 0, 148: 0, 149: 0, 150: 0, 151: 0, 152: 0, 153: 0, 155: 0, 156: 0, 157: 0, 158: 0, 159: 0, 160: 0, 161: 0, 162: 0, 163: 0, 164: 0, 165: 0, 166: 0, 167: 0, 168: 0, 169: 0, 170: 0, 171: 0, 172: 0, 173: 0, 174: 0, 175: 0, 176: 0, 177: 0, 178: 0, 179: 0, 180: 0, 181: 0, 182: 0, 183: 0, 184: 0, 185: 0, 186: 0, 187: 0, 188: 0, 189: 0, 190: 0, 191: 0, 192: 0, 193: 0, 194: 0, 195: 0, 196: 0, 197: 0, 198: 0, 199: 1, 200: 0, 201: 0, 202: 0, 203: 0, 204: 0, 205: 0, 206: 0, 207: 0, 208: 0, 209: 0, 210: 0, 211: 0, 212: 0, 213: 0, 214: 0, 215: 0, 216: 0, 217: 0, 218: 0, 219: 0, 220: 0, 221: 0, 222: 0, 223: 0, 224: 0, 225: 0, 226: 0, 227: 0, 228: 0, 229: 0, 230: 0, 231: 0, 232: 0, 233: 0, 234: 0, 235: 0, 236: 0, 237: 0, 238: 0, 239: 0, 240: 0, 241: 0, 242: 0, 243: 0, 244: 0, 245: 0, 246: 0, 247: 0, 248: 0, 249: 0, 250: 0, 251: 0, 252: 0, 253: 0, 254: 0, 255: 0, 256: 0, 257: 0, 258: 0, 259: 0, 260: 0, 261: 0, 262: 0, 263: 0, 264: 0, 265: 0, 266: 0, 267: 0, 268: 0, 269: 0, 270: 0, 271: 0, 272: 0, 273: 0, 274: 0, 275: 0, 276: 0, 277: 0, 278: 0, 279: 0, 280: 0, 281: 0, 282: 0, 283: 0, 284: 0, 285: 0, 286: 0, 288: 0, 289: 0, 290: 0, 291: 0, 292: 0, 293: 0, 294: 0, 295: 0, 296: 0, 298: 0, 299: 0, 300: 0, 301: 0, 302: 0, 303: 0, 304: 0, 306: 0, 307: 0, 309: 0, 311: 0, 312: 0, 313: 0, 314: 0, 315: 0, 316: 0, 317: 0, 318: 0, 320: 0, 321: 0, 322: 0, 323: 0, 325: 0, 326: 0, 327: 0, 328: 0, 330: 0, 331: 0, 332: 0, 333: 0, 334: 0, 336: 0, 337: 0, 338: 0, 339: 0, 340: 0, 341: 0, 342: 0, 343: 0, 344: 0, 345: 0, 346: 0, 348: 0, 349: 0, 351: 0, 353: 0, 354: 0, 355: 0, 356: 0, 358: 0, 359: 0, 360: 0, 362: 0, 363: 0, 364: 0, 365: 0, 366: 0, 367: 0, 368: 0, 369: 0, 370: 0, 371: 0, 372: 0, 373: 0, 374: 0, 375: 0, 377: 0, 378: 0, 379: 0, 380: 0, 381: 0, 382: 0, 383: 0, 385: 0, 386: 0, 387: 0, 388: 0, 390: 0, 391: 0, 392: 0, 393: 0, 395: 0, 397: 0, 398: 0, 399: 0, 400: 0, 402: 0, 405: 0, 408: 0, 409: 1, 413: 0, 414: 0, 415: 0, 416: 0, 417: 0, 418: 0, 419: 0, 421: 0, 422: 0, 425: 0, 426: 0, 427: 0, 428: 0, 429: 0, 430: 0, 432: 0, 433: 0, 434: 0, 439: 0, 440: 0, 441: 0, 442: 0, 447: 0, 448: 0, 449: 0, 450: 0, 452: 0, 453: 0, 454: 0, 456: 0, 458: 0, 459: 0, 460: 0, 462: 0, 463: 0, 464: 0, 465: 0, 466: 0, 467: 0, 469: 0, 472: 0, 473: 0, 474: 0, 475: 0, 477: 0, 478: 0, 479: 0, 480: 0, 481: 0, 482: 0, 483: 0, 484: 0, 485: 0, 486: 0, 487: 0, 490: 0, 491: 0, 492: 0, 493: 0, 494: 0, 496: 0, 497: 0, 499: 0, >500: 32, 500: 0

Sig_18_Blood.deconflicted_germline 3: 0, 7: 0, 9: 0, 28: 0, 30: 0, 43: 0, 45: 0, 47: 0, 48: 0, 52: 0, 57: 0, 59: 0, 60: 0, 63: 0, 65: 0, 66: 0, 68: 0, 74: 0, 75: 0, 77: 0, 78: 0, 81: 0, 83: 0, 84: 0, 85: 0, 87: 0, 88: 0, 89: 0, 92: 0, 93: 0, 94: 0, 95: 0, 97: 0, 98: 0, 101: 0, 102: 0, 104: 0, 106: 0, 107: 0, 109: 0, 110: 0, 112: 0, 113: 0, 114: 0, 115: 0, 116: 0, 117: 0, 118: 0, 119: 0, 120: 1, 121: 0, 122: 0, 123: 0, 124: 0, 125: 0, 126: 0, 127: 0, 128: 0, 129: 0, 130: 0, 131: 0, 132: 0, 133: 0, 134: 0, 135: 0, 136: 0, 137: 0, 138: 0, 139: 0, 140: 0, 142: 0, 143: 0, 144: 0, 145: 0, 146: 0, 147: 0, 148: 0, 149: 0, 150: 0, 151: 0, 152: 0, 153: 0, 155: 0, 156: 0, 157: 0, 158: 0, 159: 0, 160: 0, 161: 0, 162: 0, 163: 0, 164: 0, 165: 0, 166: 0, 167: 0, 168: 0, 169: 0, 170: 0, 171: 0, 172: 0, 173: 0, 174: 0, 175: 0, 176: 0, 177: 0, 178: 0, 179: 0, 180: 0, 181: 0, 182: 0, 183: 0, 184: 0, 185: 0, 186: 0, 187: 0, 188: 0, 189: 0, 190: 0, 191: 0, 192: 0, 193: 0, 194: 0, 195: 0, 196: 0, 197: 0, 198: 0, 199: 0, 200: 0, 201: 0, 202: 0, 203: 0, 204: 0, 205: 0, 206: 0, 207: 0, 208: 0, 209: 0, 210: 0, 211: 0, 212: 0, 213: 0, 214: 0, 215: 0, 216: 0, 217: 0, 218: 0, 219: 1, 220: 0, 221: 0, 222: 0, 223: 0, 224: 0, 225: 0, 226: 0, 227: 0, 228: 0, 229: 0, 230: 0, 231: 0, 232: 0, 233: 0, 234: 1, 235: 0, 236: 0, 237: 0, 238: 0, 239: 0, 240: 0, 241: 0, 242: 0, 243: 0, 244: 0, 245: 0, 246: 0, 247: 0, 248: 0, 249: 0, 250: 0, 251: 0, 252: 0, 253: 0, 254: 0, 255: 0, 256: 0, 257: 0, 258: 0, 259: 0, 260: 0, 261: 0, 262: 0, 263: 0, 264: 0, 265: 0, 266: 0, 267: 0, 268: 0, 269: 0, 270: 0, 271: 0, 272: 0, 273: 0, 274: 0, 275: 0, 276: 0, 277: 0, 278: 0, 279: 0, 280: 0, 281: 0, 282: 0, 283: 0, 284: 0, 285: 0, 286: 0, 288: 0, 289: 0, 290: 0, 291: 0, 292: 0, 293: 0, 294: 0, 295: 0, 296: 0, 298: 0, 299: 0, 300: 0, 301: 0, 302: 0, 303: 0, 304: 0, 306: 0, 307: 0, 309: 0, 311: 0, 312: 0, 313: 0, 314: 0, 315: 0, 316: 0, 317: 0, 318: 0, 320: 0, 321: 0, 322: 0, 323: 0, 325: 0, 326: 0, 327: 0, 328: 0, 330: 0, 331: 0, 332: 0, 333: 0, 334: 0, 336: 0, 337: 0, 338: 0, 339: 0, 340: 0, 341: 0, 342: 0, 343: 0, 344: 0, 345: 0, 346: 0, 348: 0, 349: 0, 351: 0, 353: 0, 354: 0, 355: 0, 356: 0, 358: 0, 359: 0, 360: 0, 362: 0, 363: 0, 364: 0, 365: 0, 366: 0, 367: 0, 368: 0, 369: 0, 370: 0, 371: 0, 372: 0, 373: 0, 374: 0, 375: 0, 377: 0, 378: 0, 379: 0, 380: 0, 381: 0, 382: 0, 383: 0, 385: 0, 386: 0, 387: 0, 388: 0, 390: 0, 391: 0, 392: 0, 393: 0, 395: 0, 397: 0, 398: 0, 399: 0, 400: 0, 402: 0, 405: 0, 408: 0, 409: 0, 413: 0, 414: 0, 415: 0, 416: 0, 417: 0, 418: 0, 419: 0, 421: 0, 422: 0, 425: 0, 426: 0, 427: 0, 428: 0, 429: 0, 430: 0, 432: 0, 433: 0, 434: 0, 439: 0, 440: 0, 441: 0, 442: 0, 447: 0, 448: 0, 449: 0, 450: 0, 452: 0, 453: 0, 454: 0, 456: 0, 458: 0, 459: 0, 460: 0, 462: 0, 463: 0, 464: 0, 465: 0, 466: 0, 467: 0, 469: 0, 472: 0, 473: 0, 474: 0, 475: 0, 477: 0, 478: 0, 479: 0, 480: 0, 481: 0, 482: 0, 483: 0, 484: 0, 485: 0, 486: 0, 487: 0, 490: 0, 491: 0, 492: 0, 493: 0, 494: 0, 496: 0, 497: 0, 499: 0, >500: 24, 500: 0

custom_Sig_18_tumor_normal.strelka.somatic_snvs 3: 0, 7: 0, 9: 0, 28: 0, 30: 0, 43: 0, 45: 0, 47: 0, 48: 0, 52: 0, 57: 0, 59: 0, 60: 0, 63: 0, 65: 0, 66: 0, 68: 0, 74: 0, 75: 0, 77: 0, 78: 0, 81: 0, 83: 0, 84: 0, 85: 0, 87: 0, 88: 0, 89: 0, 92: 0, 93: 0, 94: 0, 95: 0, 97: 0, 98: 0, 101: 0, 102: 0, 104: 0, 106: 0, 107: 0, 109: 0, 110: 0, 112: 0, 113: 0, 114: 0, 115: 0, 116: 0, 117: 0, 118: 0, 119: 0, 120: 0, 121: 0, 122: 0, 123: 0, 124: 0, 125: 0, 126: 0, 127: 0, 128: 0, 129: 0, 130: 0, 131: 0, 132: 0, 133: 0, 134: 0, 135: 0, 136: 0, 137: 0, 138: 0, 139: 0, 140: 0, 142: 0, 143: 0, 144: 0, 145: 0, 146: 0, 147: 0, 148: 0, 149: 0, 150: 0, 151: 0, 152: 0, 153: 0, 155: 0, 156: 0, 157: 0, 158: 0, 159: 0, 160: 0, 161: 0, 162: 0, 163: 0, 164: 0, 165: 0, 166: 0, 167: 0, 168: 0, 169: 0, 170: 0, 171: 0, 172: 0, 173: 0, 174: 0, 175: 0, 176: 0, 177: 0, 178: 0, 179: 0, 180: 0, 181: 0, 182: 0, 183: 0, 184: 0, 185: 0, 186: 0, 187: 0, 188: 0, 189: 0, 190: 0, 191: 0, 192: 0, 193: 0, 194: 0, 195: 0, 196: 0, 197: 0, 198: 0, 199: 0, 200: 0, 201: 0, 202: 0, 203: 0, 204: 0, 205: 0, 206: 0, 207: 0, 208: 0, 209: 0, 210: 0, 211: 0, 212: 0, 213: 0, 214: 0, 215: 0, 216: 0, 217: 0, 218: 0, 219: 0, 220: 0, 221: 0, 222: 0, 223: 0, 224: 0, 225: 0, 226: 0, 227: 0, 228: 0, 229: 0, 230: 0, 231: 0, 232: 0, 233: 0, 234: 0, 235: 0, 236: 0, 237: 0, 238: 0, 239: 0, 240: 0, 241: 0, 242: 0, 243: 0, 244: 0, 245: 0, 246: 0, 247: 0, 248: 0, 249: 0, 250: 0, 251: 0, 252: 0, 253: 0, 254: 0, 255: 0, 256: 0, 257: 0, 258: 0, 259: 0, 260: 0, 261: 0, 262: 0, 263: 0, 264: 0, 265: 0, 266: 0, 267: 0, 268: 0, 269: 0, 270: 0, 271: 0, 272: 0, 273: 0, 274: 0, 275: 0, 276: 0, 277: 0, 278: 0, 279: 0, 280: 0, 281: 0, 282: 0, 283: 0, 284: 0, 285: 0, 286: 0, 288: 0, 289: 0, 290: 0, 291: 0, 292: 0, 293: 0, 294: 0, 295: 0, 296: 0, 298: 0, 299: 0, 300: 0, 301: 0, 302: 0, 303: 0, 304: 0, 306: 0, 307: 0, 309: 0, 311: 0, 312: 0, 313: 0, 314: 0, 315: 0, 316: 0, 317: 0, 318: 0, 320: 0, 321: 0, 322: 0, 323: 0, 325: 0, 326: 0, 327: 0, 328: 0, 330: 0, 331: 0, 332: 0, 333: 0, 334: 0, 336: 0, 337: 0, 338: 0, 339: 0, 340: 0, 341: 0, 342: 0, 343: 0, 344: 0, 345: 0, 346: 0, 348: 0, 349: 0, 351: 0, 353: 0, 354: 0, 355: 0, 356: 0, 358: 0, 359: 0, 360: 0, 362: 0, 363: 0, 364: 0, 365: 0, 366: 0, 367: 0, 368: 0, 369: 0, 370: 0, 371: 0, 372: 0, 373: 0, 374: 0, 375: 0, 377: 0, 378: 0, 379: 0, 380: 0, 381: 0, 382: 0, 383: 0, 385: 0, 386: 0, 387: 0, 388: 0, 390: 0, 391: 0, 392: 0, 393: 0, 395: 0, 397: 0, 398: 0, 399: 0, 400: 0, 402: 0, 405: 0, 408: 0, 409: 0, 413: 0, 414: 0, 415: 0, 416: 0, 417: 0, 418: 0, 419: 0, 421: 0, 422: 0, 425: 0, 426: 0, 427: 0, 428: 0, 429: 0, 430: 0, 432: 0, 433: 0, 434: 0, 439: 0, 440: 0, 441: 0, 442: 0, 447: 0, 448: 0, 449: 0, 450: 0, 452: 0, 453: 0, 454: 0, 456: 0, 458: 0, 459: 0, 460: 0, 462: 0, 463: 0, 464: 0, 465: 0, 466: 0, 467: 0, 469: 0, 472: 0, 473: 0, 474: 0, 475: 0, 477: 0, 478: 0, 479: 0, 480: 0, 481: 0, 482: 0, 483: 0, 484: 0, 485: 0, 486: 0, 487: 0, 490: 0, 491: 0, 492: 0, 493: 0, 494: 0, 496: 0, 497: 0, 499: 0, >500: 65, 500: 0

----------------------

Tool: Vcftools
Section: TsTv by Count
Section description: Plot of <code>TSTV-BY-COUNT</code> - the transition to transversion ratio as a function of alternative allele count from the output of vcftools TsTv-by-count.
Section help text: <code>Transition</code> is a purine-to-purine or pyrimidine-to-pyrimidine point mutations.
<code>Transversion</code> is a purine-to-pyrimidine or pyrimidine-to-purine point mutation.
<code>Alternative allele count</code> is the number of alternative alleles at the site.
Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.)
Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on <code>--TsTv-by-count</code>
Title: VCFTools: TsTv by Count

Plot type: x/y line
X axis: Alternative Allele Count
Y axis: TsTv Ratio

Samples: HCC1395_BL.TsTv.count, HCC1395_BL.deconflicted_germline.TsTv.count, HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.TsTv.count, HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.TsTv.count, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.TsTv.count, HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.TsTv.count, Sig_18_Blood.TsTv.count, Sig_18_Blood.deconflicted_germline.TsTv.count, custom_Sig_18_tumor_normal.manta.diploid_sv.TsTv.count, custom_Sig_18_tumor_normal.manta.somatic_sv.TsTv.count, custom_Sig_18_tumor_normal.strelka.somatic_indels.TsTv.count, custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.count

HCC1395_BL.TsTv.count 0: N/A, 1: N/A

HCC1395_BL.deconflicted_germline.TsTv.count 0: N/A, 1: 3

HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.TsTv.count 0: N/A, 1: N/A

HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.TsTv.count 0: N/A, 1: N/A, 2: N/A, 3: N/A

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.TsTv.count 0: N/A, 1: N/A, 2: N/A, 3: N/A

HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.TsTv.count 0: 1, 1: N/A, 2: N/A, 3: N/A

Sig_18_Blood.TsTv.count 0: N/A, 1: N/A

Sig_18_Blood.deconflicted_germline.TsTv.count 0: N/A, 1: 3

custom_Sig_18_tumor_normal.manta.diploid_sv.TsTv.count 0: N/A, 1: N/A

custom_Sig_18_tumor_normal.manta.somatic_sv.TsTv.count 0: N/A, 1: N/A, 2: N/A, 3: N/A

custom_Sig_18_tumor_normal.strelka.somatic_indels.TsTv.count 0: N/A, 1: N/A, 2: N/A, 3: N/A

custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.count 0: 1, 1: N/A, 2: N/A, 3: N/A

----------------------

Tool: Vcftools
Section: TsTv by Qual
Section description: Plot of <code>TSTV-BY-QUAL</code> - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.
Section help text: <code>Transition</code> is a purine-to-purine or pyrimidine-to-pyrimidine point mutations.
<code>Transversion</code> is a purine-to-pyrimidine or pyrimidine-to-purine point mutation.
<code>Quality</code> here is the Phred-scaled quality score as given in the QUAL column of VCF.
Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.)
Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on <code>--TsTv-by-qual</code>
Title: VCFTools: TsTv by Qual

Plot type: x/y line
X axis: SNP Quality Threshold
Y axis: TsTv Ratio

Samples: HCC1395_BL.deconflicted_germline.TsTv.qual, Sig_18_Blood.deconflicted_germline.TsTv.qual

HCC1395_BL.deconflicted_germline.TsTv.qual 67: 3, 136: 3, 256: 3, 497: 3, 627: 3, 645: 3, 695: 3, 712: 3, 747: 3, 790: 3, 796: 3, 813: 3, 946: 3, 1,021: 3, 1,057: 3, 1,078: 3, 1,096: 3, 1,159: 3, 1,177: 3, 1,188: 3, 1,189: 3, 1,209: 3, 1,216: 3, 1,221: 3, 1,293: 3, 1,334: 3, 1,362: 3, 1,369: 3, 1,370: 3, 1,371: 3, 1,390: 3, 1,396: 3, 1,399: 3, 1,400: 3, 1,402: 3, 1,446: 3, 1,457: 3, 1,461: 3, 1,522: 3, 1,551: 3, 1,553: 3, 1,576: 3, 1,591: 3, 1,593: 3, 1,624: 3, 1,639: 3, 1,656: 3, 1,667: 3, 1,669: 3, 1,676: 3, 1,677: 3, 1,680: 3, 1,697: 3, 1,699: 3, 1,725: 3, 1,729: 3, 1,730: 3, 1,764: 3, 1,791: 3, 1,816: 3, 1,817: 3, 1,836: 3, 1,838: 3, 1,863: 3, 1,868: 3, 1,880: 3, 1,885: 3, 1,896: 3, 1,916: 3, 1,924: 3, 1,939: 3, 1,952: 3, 1,966: 3, 1,980: 3, 2,038: 3, 2,070: 3, 2,094: 3, 2,123: 3, 2,139: 3, 2,144: 3, 2,163: 3, 2,182: 3, 2,183: 3, 2,184: 3, 2,196: 3, 2,197: 3, 2,220: 3, 2,229: 3, 2,238: 3, 2,246: 3, 2,258: 3, 2,266: 3, 2,268: 3, 2,273: 3, 2,279: 3, 2,294: 3, 2,309: 3, 2,312: 3, 2,323: 3, 2,325: 3, 2,343: 3, 2,366: 3, 2,377: 3, 2,379: 3, 2,391: 3, 2,401: 3, 2,402: 3, 2,406: 3, 2,415: 3, 2,476: 3, 2,480: 3, 2,484: 3, 2,513: 3, 2,535: 3, 2,562: 3, 2,596: 3, 2,612: 3, 2,620: 3, 2,635: 3, 2,655: 3, 2,657: 3, 2,678: 3, 2,684: 3, 2,685: 3, 2,714: 3, 2,725: 3, 2,751: 3, 2,753: 3, 2,772: 3, 2,792: 3, 2,800: 3, 2,828: 3, 2,862: 3, 2,875: 3, 2,882: 3, 2,894: 3, 2,911: 3, 2,938: 3, 2,940: 3, 2,955: 3, 2,961: 3, 3,000: 3, 3,004: 3, 3,027: 3, 3,054: 3, 3,101: 3, 3,102: 3, 3,107: 3, 3,117: 3, 3,128: 3, 3,154: 3, 3,160: 3, 3,166: 3, 3,179: 2, 3,204: 2, 3,209: 2, 3,224: 2, 3,260: 2, 3,262: 2, 3,290: 2, 3,314: 2, 3,337: 2, 3,347: 2, 3,460: 2, 3,482: 2, 3,489: 2, 3,505: 2, 3,511: 3, 3,546: 3, 3,573: 3, 3,576: 3, 3,592: 3, 3,652: 3, 3,674: 3, 3,684: 3, 3,716: 3, 3,718: 3, 3,787: 3, 3,860: 3, 3,894: 3, 3,897: 3, 3,899: 3, 3,905: 3, 3,948: 3, 3,953: 3, 4,031: 3, 4,043: 3, 4,077: 3, 4,078: 3, 4,084: 3, 4,096: 3, 4,119: 3, 4,129: 3, 4,173: 3, 4,187: 3, 4,195: 3, 4,199: 3, 4,305: 3, 4,308: 3, 4,317: 3, 4,318: 3, 4,337: 3, 4,350: 3, 4,353: 3, 4,746: 2, 4,873: 2, 4,909: 2, 4,963: 2, 4,999: 2, 5,107: 3, 5,228: 3, 5,307: 3, 5,319: 3, 5,414: 3, 5,427: 3, 5,559: 2, 5,783: 2, 5,810: 2, 5,815: 2, 5,828: 2, 5,830: 2, 5,840: 2, 5,874: 2, 5,941: 2, 5,945: 2, 5,946: 2, 6,136: 2, 6,202: 2, 6,209: 2, 6,254: 2, 6,379: 3, 6,425: 2, 6,443: 2, 6,505: 2, 6,642: 2, 6,643: 2, 6,696: 2, 6,715: 2, 6,738: 2, 6,834: 2, 6,869: 2, 6,908: 2, 6,960: 2, 6,991: 2, 7,016: 2, 7,067: 2, 7,095: 2, 7,115: 2, 7,212: 2, 7,290: 2, 7,424: 2, 7,484: 2, 7,634: 2, 7,675: 2, 7,745: 2, 7,805: 2, 7,890: 2, 8,022: 2, 8,158: 2, 8,177: 2, 8,265: 2, 8,363: 2, 8,413: 2, 8,541: 2, 8,615: 2, 8,759: 2, 8,921: 2, 8,971: 2, 9,018: 2, 9,202: 2, 9,805: 2, 9,808: 2, 10,273: 2, 10,330: 2, 10,454: 2, 10,545: 2, 10,620: 2, 10,755: 2, 10,759: 2, 10,992: 2, 11,396: 2, 12,335: 2, 12,363: 2, 12,445: 2, 12,844: 2, 13,010: 2, 13,055: 2, 13,404: 2, 13,678: 2, 13,698: 2, 13,733: 2, 13,917: 2, 14,232: 2, 14,717: 1, 14,850: 1, 15,064: 2, 15,130: 1, 15,162: 1, 15,237: 1, 15,314: 1, 15,344: 1, 15,455: 1, 15,512: 1, 15,700: 1, 15,768: 1, 15,890: 1, 15,906: 1, 16,364: 1, 16,646: 1, 16,768: 1, 16,963: 1, 17,632: 1, 19,297: 2, 19,552: 2, 20,547: 2, 20,746: 2, 22,296: 1, 30,980: 1, 33,076: 1, 33,625: 1, 35,238: 1, 35,448: 1, 35,756: 0, 36,250: 1, 37,861: 2, 38,715: 1, 43,226: N/A, 45,045: 0

Sig_18_Blood.deconflicted_germline.TsTv.qual 48: 2, 226: 2, 434: 2, 466: 2, 469: 2, 506: 2, 701: 3, 755: 3, 786: 3, 830: 2, 1,122: 2, 1,133: 2, 1,139: 3, 1,206: 2, 1,216: 2, 1,266: 2, 1,298: 2, 1,312: 2, 1,315: 2, 1,316: 2, 1,372: 2, 1,404: 2, 1,430: 2, 1,437: 2, 1,560: 2, 1,585: 2, 1,588: 2, 1,599: 2, 1,610: 2, 1,632: 2, 1,640: 2, 1,675: 2, 1,676: 2, 1,696: 2, 1,728: 2, 1,750: 2, 1,790: 2, 1,802: 2, 1,803: 2, 1,847: 2, 1,867: 2, 1,925: 2, 1,931: 2, 1,945: 2, 1,948: 2, 1,959: 2, 1,961: 2, 1,965: 2, 1,973: 2, 1,978: 2, 2,053: 2, 2,074: 2, 2,076: 2, 2,109: 2, 2,148: 2, 2,152: 2, 2,179: 2, 2,190: 2, 2,234: 2, 2,252: 2, 2,310: 2, 2,322: 2, 2,332: 2, 2,336: 2, 2,367: 2, 2,415: 2, 2,422: 2, 2,427: 2, 2,460: 2, 2,472: 2, 2,490: 2, 2,495: 2, 2,499: 2, 2,518: 2, 2,540: 2, 2,557: 2, 2,572: 2, 2,594: 2, 2,606: 2, 2,612: 2, 2,641: 2, 2,654: 2, 2,664: 2, 2,697: 2, 2,725: 2, 2,735: 2, 2,745: 2, 2,771: 2, 2,776: 2, 2,816: 2, 2,832: 2, 2,848: 2, 2,885: 2, 2,907: 2, 2,963: 2, 2,986: 2, 2,990: 2, 3,003: 2, 3,004: 2, 3,010: 2, 3,063: 2, 3,071: 2, 3,123: 2, 3,138: 2, 3,151: 2, 3,177: 2, 3,243: 2, 3,322: 2, 3,328: 2, 3,355: 2, 3,375: 2, 3,389: 2, 3,404: 2, 3,431: 2, 3,449: 2, 3,451: 2, 3,457: 2, 3,465: 2, 3,466: 2, 3,509: 2, 3,534: 2, 3,537: 2, 3,542: 2, 3,543: 2, 3,586: 2, 3,619: 2, 3,627: 2, 3,632: 2, 3,653: 2, 3,658: 2, 3,667: 2, 3,674: 2, 3,738: 2, 3,801: 2, 3,823: 2, 3,851: 2, 3,872: 2, 3,891: 2, 3,907: 2, 3,911: 2, 3,942: 2, 3,949: 2, 4,020: 2, 4,056: 2, 4,083: 2, 4,102: 2, 4,123: 2, 4,168: 2, 4,208: 2, 4,310: 2, 4,316: 2, 4,366: 2, 4,373: 2, 4,384: 2, 4,420: 2, 4,440: 2, 4,474: 2, 4,594: 2, 4,655: 2, 4,659: 2, 4,727: 2, 4,747: 2, 4,761: 2, 4,787: 2, 4,804: 2, 4,806: 2, 4,836: 2, 4,838: 2, 4,880: 2, 4,914: 2, 4,921: 2, 4,979: 2, 5,008: 2, 5,038: 2, 5,040: 2, 5,048: 2, 5,099: 2, 5,144: 2, 5,205: 2, 5,218: 2, 5,219: 2, 5,303: 2, 5,321: 2, 5,377: 2, 5,398: 2, 5,405: 2, 5,484: 2, 5,515: 2, 5,586: 2, 5,606: 2, 5,649: 2, 5,716: 2, 5,750: 2, 5,763: 2, 5,829: 2, 5,831: 2, 5,858: 2, 5,902: 2, 5,917: 2, 5,986: 2, 5,991: 2, 6,012: 2, 6,090: 2, 6,104: 2, 6,173: 2, 6,292: 2, 6,424: 2, 6,527: 2, 6,563: 2, 6,578: 2, 6,637: 2, 6,687: 2, 6,737: 2, 6,750: 2, 6,785: 2, 6,808: 2, 6,846: 2, 6,888: 2, 6,989: 2, 7,029: 2, 7,159: 2, 7,195: 2, 7,197: 2, 7,214: 2, 7,608: 2, 7,612: 2, 7,657: 2, 7,724: 2, 7,729: 2, 7,743: 2, 7,756: 2, 7,758: 2, 7,765: 2, 7,824: 2, 7,896: 2, 7,897: 2, 7,907: 2, 8,005: 2, 8,039: 2, 8,156: 2, 8,196: 2, 8,206: 2, 8,297: 2, 8,377: 2, 8,399: 2, 8,512: 2, 8,728: 2, 8,814: 2, 8,868: 2, 8,886: 2, 8,974: 2, 8,986: 2, 8,995: 2, 9,003: 2, 9,077: 2, 9,080: 2, 9,100: 2, 9,200: 2, 9,252: 2, 9,295: 2, 9,360: 2, 9,428: 2, 9,430: 2, 9,471: 2, 9,510: 2, 9,801: 2, 9,836: 2, 9,845: 2, 10,215: 2, 10,218: 2, 10,624: 2, 10,648: 2, 10,996: 2, 11,042: 2, 11,044: 2, 11,093: 2, 11,123: 2, 11,157: 2, 11,160: 2, 11,239: 2, 11,258: 2, 11,415: 2, 11,498: 2, 11,534: 2, 11,986: 2, 12,052: 2, 12,252: 2, 12,504: 2, 12,651: 2, 12,967: 2, 13,256: 2, 13,678: 2, 13,924: 2, 13,974: 2, 14,299: 2, 14,494: 2, 14,737: 2, 14,970: 2, 15,014: 2, 15,114: 2, 15,212: 2, 15,685: 2, 16,266: 2, 16,891: 2, 19,080: 2, 19,368: 2, 19,596: 2, 19,614: 2, 19,672: 2, 19,747: 2, 19,972: 2, 20,130: 2, 20,370: 2, 20,856: 2, 22,260: 2, 22,326: 2, 22,364: 2, 22,627: 2, 22,950: 2, 23,431: 2, 23,530: 2, 23,724: 2, 24,058: 2, 24,190: 2, 24,212: 2, 24,214: 2, 24,220: 2, 24,361: 2, 24,370: 2, 24,435: 2, 24,545: 2, 24,814: 2, 24,960: 2, 25,129: 2, 25,442: 2, 25,852: 2, 26,357: 1, 26,652: 2, 27,417: 2, 29,525: 2, 29,882: 2, 29,980: 2, 32,910: 1, 33,062: 1, 33,938: 1, 34,069: 1, 34,328: 1, 36,259: 1, 37,204: 1, 47,751: 1, 47,882: 1, 52,466: 1, 53,968: 1, 54,930: 0, 55,183: 1, 56,418: 0, 56,908: 0, 61,335: 0, 61,723: 0, 64,326: 0, 71,283: 0, 73,424: 0, 75,217: N/A

----------------------

Tool: SNPeff
Section: Variants by Genomic Region
Section description: The stacked bar plot shows locations of detected variants in
the genome and the number of variants for each location.
Section help text: The upstream and downstream interval size to detect these
genomic regions is 5000bp by default.
Title: SnpEff: Counts by Genomic Region

Plot type: bar plot
Values: # Reads

|Sample|Intron|Exon|Upstream|Downstream|Transcript|Splice Site Region|UTR 3 Prime|UTR 5 Prime|Intergenic|
|---|---|---|---|---|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff|180|83|39|33|22|9|9|5|1|
|custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff|66|19|13|13|5|9|2|1|1|
|custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff|2|1|2|1|1|nan|nan|nan|nan|
|Sig_18_Blood_custom.ann_snpEff|3|8|1|1|nan|1|nan|nan|nan|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff|142|319|45|47|31|6|7|8|nan|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff|219|105|45|34|23|11|10|5|2|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff|32|7|6|8|4|5|2|1|nan|
|HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff|1|nan|nan|nan|nan|nan|nan|nan|nan|
|HCC1395_BL_custom.ann_snpEff|3|8|1|1|nan|1|nan|nan|nan|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff|126|289|42|50|28|2|6|6|nan|

----------------------

Tool: SNPeff
Section: Variant Effects by Impact
Section description: The stacked bar plot shows the putative impact of detected
variants and the number of variants for each impact.
Section help text: There are four levels of impacts predicted by SnpEff:
<ul>
<li><strong>High</strong>: High impact (like stop codon)</li>
<li><strong>Moderate</strong>: Middle impact (like same type of amino acid substitution)</li>
<li><strong>Low</strong>: Low impact (ie silence mutation)</li>
<li><strong>Modifier</strong>: No impact</li>
</ul>
Title: SnpEff: Counts by Effects Impact

Plot type: bar plot
Values: # Reads

|Sample|Modifier|Low|Moderate|High|
|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff|293|34|52|2|
|custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff|104|9|8|8|
|custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff|6|nan|1|12|
|Sig_18_Blood_custom.ann_snpEff|5|1|nan|10|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff|301|139|156|9|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff|349|45|58|4|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff|54|5|6|nan|
|HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff|nan|nan|nan|8|
|HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff|1|nan|nan|8|
|HCC1395_BL_custom.ann_snpEff|5|1|nan|10|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff|271|131|141|6|

----------------------

Tool: SNPeff
Section: Variants by Effect Types
Section description: The stacked bar plot shows the effect of variants at protein
level and the number of variants for each effect type.
Section help text: This plot shows the effect of variants with respect to
the mRNA.
Title: SnpEff: Counts by Effect Types

Plot type: bar plot
Values: # Reads

|Sample|Intron Variant|Missense Variant|Upstream Gene Variant|Downstream Gene Variant|Synonymous Variant|Intragenic Variant|Splice Region Variant|3 Prime UTR Variant|Non Coding Transcript Exon Variant|5 Prime UTR Variant|Stop Gained|5 Prime UTR Premature Start Codon Gain Variant|Intergenic Region|
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff|189|52|39|33|24|22|12|9|5|4|2|1|1|
|custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff|75|nan|13|13|nan|5|9|2|3|1|nan|nan|1|
|custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff|2|nan|2|1|nan|1|nan|nan|nan|nan|nan|nan|nan|
|Sig_18_Blood_custom.ann_snpEff|3|nan|1|1|nan|nan|1|nan|1|nan|nan|nan|nan|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff|142|149|45|47|134|31|8|7|24|7|2|1|nan|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff|231|58|45|34|35|23|11|10|11|5|1|nan|2|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff|37|nan|6|8|nan|3|5|2|1|1|nan|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff|1|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|
|HCC1395_BL_custom.ann_snpEff|3|nan|1|1|nan|nan|1|nan|1|nan|nan|nan|nan|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff|126|135|42|50|130|28|4|6|14|6|1|nan|nan|

----------------------

Tool: SNPeff
Section: Variants by Functional Class
Section description: The stacked bar plot shows the effect of variants and
the number of variants for each effect type.
Section help text: This plot shows the effect of variants on the translation of
the mRNA as protein. There are three possible cases:
<ul>
<li><strong>Silent</strong>: The amino acid does not change.</li>
<li><strong>Missense</strong>: The amino acid is different.</li>
<li><strong>Nonsense</strong>: The variant generates a stop codon.</li>
</ul>
Title: SnpEff: Counts by Functional Class

Plot type: bar plot
Values: # Reads

|Sample|Nonsense|Silent|Missense|
|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff|2|24|52|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff|2|134|149|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff|1|35|59|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff|1|130|135|

----------------------

Tool: SNPeff
Section: Variant Qualities
Section description: The line plot shows the quantity as function of the
variant quality score.
Section help text: The quality score corresponds to the QUAL column of the
VCF file. This score is set by the variant caller.
Title: SnpEff: Qualities

Plot type: x/y line
X axis: Values
Y axis: Count

Samples: HCC1395_BL.deconflicted_germline_custom.ann_snpEff, HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff, Sig_18_Blood.deconflicted_germline_custom.ann_snpEff, custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff

HCC1395_BL.deconflicted_germline_custom.ann_snpEff 67: 1, 256: 1, 497: 1, 645: 1, 712: 1, 790: 1, 796: 1, 946: 1, 1,057: 1, 1,096: 1, 1,159: 1, 1,188: 1, 1,209: 1, 1,216: 1, 1,293: 1, 1,362: 1, 1,370: 1, 1,371: 1, 1,396: 1, 1,400: 1, 1,446: 1, 1,457: 1, 1,474: 1, 1,522: 1, 1,547: 1, 1,553: 1, 1,591: 1, 1,624: 1, 1,639: 1, 1,667: 1, 1,676: 1, 1,680: 1, 1,697: 1, 1,725: 1, 1,730: 1, 1,791: 1, 1,816: 1, 1,836: 1, 1,861: 1, 1,863: 1, 1,880: 1, 1,896: 1, 1,924: 1, 1,939: 1, 1,966: 1, 2,038: 1, 2,094: 1, 2,123: 1, 2,144: 1, 2,182: 1, 2,183: 1, 2,196: 1, 2,220: 1, 2,238: 1, 2,246: 1, 2,266: 1, 2,273: 1, 2,294: 1, 2,309: 1, 2,323: 1, 2,343: 1, 2,366: 1, 2,379: 1, 2,401: 1, 2,406: 1, 2,415: 1, 2,480: 1, 2,507: 1, 2,535: 1, 2,562: 1, 2,612: 1, 2,635: 1, 2,655: 1, 2,678: 1, 2,685: 1, 2,725: 1, 2,751: 1, 2,772: 1, 2,800: 1, 2,862: 1, 2,875: 1, 2,894: 1, 2,938: 1, 2,940: 1, 2,961: 1, 3,004: 1, 3,054: 1, 3,101: 1, 3,107: 1, 3,128: 1, 3,160: 1, 3,166: 1, 3,204: 1, 3,224: 1, 3,260: 1, 3,290: 1, 3,314: 1, 3,347: 2, 3,460: 1, 3,489: 1, 3,511: 1, 3,573: 1, 3,576: 1, 3,652: 1, 3,684: 1, 3,718: 1, 3,787: 1, 3,894: 1, 3,899: 1, 3,905: 1, 3,953: 1, 4,043: 1, 4,078: 1, 4,084: 1, 4,119: 1, 4,173: 1, 4,195: 1, 4,199: 1, 4,308: 1, 4,318: 1, 4,337: 1, 4,353: 1, 4,746: 1, 4,909: 1, 4,963: 1, 4,999: 1, 5,228: 1, 5,319: 1, 5,414: 1, 5,551: 1, 5,759: 2, 5,783: 1, 5,815: 1, 5,830: 1, 5,874: 1, 5,941: 1, 5,946: 1, 6,136: 1, 6,209: 1, 6,254: 1, 6,379: 1, 6,443: 1, 6,505: 1, 6,643: 1, 6,715: 1, 6,834: 1, 6,869: 2, 6,960: 1, 7,016: 1, 7,095: 1, 7,115: 1, 7,290: 1, 7,484: 1, 7,634: 1, 7,745: 1, 7,890: 1, 8,158: 1, 8,177: 1, 8,363: 1, 8,517: 1, 8,615: 1, 8,759: 1, 8,971: 1, 9,202: 1, 9,805: 1, 10,273: 1, 10,454: 1, 10,620: 1, 10,755: 1, 10,992: 1, 11,501: 1, 12,335: 1, 12,363: 1, 12,844: 1, 13,055: 1, 13,678: 1, 13,698: 1, 13,917: 1, 14,717: 1, 14,850: 1, 15,130: 1, 15,237: 1, 15,344: 1, 15,455: 1, 15,700: 1, 15,890: 1, 16,364: 1, 16,646: 1, 16,963: 2, 18,878: 1, 19,297: 1, 20,547: 1, 21,365: 1, 22,296: 1, 30,980: 1, 33,625: 1, 35,448: 1, 36,250: 1, 37,861: 1, 43,226: 1

HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff 104: 2, 999: 1

Sig_18_Blood.deconflicted_germline_custom.ann_snpEff 48: 1, 193: 1, 434: 1, 469: 1, 701: 1, 765: 1, 830: 1, 1,133: 1, 1,206: 1, 1,216: 1, 1,298: 1, 1,315: 1, 1,372: 1, 1,430: 1, 1,560: 1, 1,588: 1, 1,610: 1, 1,640: 1, 1,676: 1, 1,696: 1, 1,750: 1, 1,802: 1, 1,827: 1, 1,867: 1, 1,925: 1, 1,931: 1, 1,948: 1, 1,961: 1, 1,973: 1, 2,050: 1, 2,074: 1, 2,097: 1, 2,148: 1, 2,179: 1, 2,234: 1, 2,290: 1, 2,322: 1, 2,335: 1, 2,367: 1, 2,422: 1, 2,460: 1, 2,490: 1, 2,495: 1, 2,518: 1, 2,557: 1, 2,594: 1, 2,612: 1, 2,654: 1, 2,697: 1, 2,735: 1, 2,771: 1, 2,816: 1, 2,832: 1, 2,885: 1, 2,963: 1, 2,990: 1, 3,004: 1, 3,063: 1, 3,123: 1, 3,138: 1, 3,177: 1, 3,322: 1, 3,355: 1, 3,389: 1, 3,431: 1, 3,451: 1, 3,465: 1, 3,509: 1, 3,537: 1, 3,543: 1, 3,619: 1, 3,632: 1, 3,658: 1, 3,674: 1, 3,801: 1, 3,823: 1, 3,872: 2, 3,907: 1, 3,941: 1, 3,949: 1, 4,056: 1, 4,102: 1, 4,168: 1, 4,310: 1, 4,366: 1, 4,384: 1, 4,440: 1, 4,594: 1, 4,659: 1, 4,747: 1, 4,787: 1, 4,806: 1, 4,836: 1, 4,880: 1, 4,921: 1, 5,008: 1, 5,040: 1, 5,099: 1, 5,205: 1, 5,219: 1, 5,321: 1, 5,398: 1, 5,484: 1, 5,586: 1, 5,649: 1, 5,750: 1, 5,829: 1, 5,858: 1, 5,902: 2, 5,986: 1, 6,012: 1, 6,104: 1, 6,292: 1, 6,527: 1, 6,578: 1, 6,687: 1, 6,750: 1, 6,808: 1, 6,888: 1, 7,029: 1, 7,195: 1, 7,214: 1, 7,612: 1, 7,657: 1, 7,729: 1, 7,743: 1, 7,758: 1, 7,824: 1, 7,897: 1, 8,005: 1, 8,156: 1, 8,206: 1, 8,297: 1, 8,377: 1, 8,512: 1, 8,728: 1, 8,868: 1, 8,974: 1, 8,995: 1, 9,077: 1, 9,100: 1, 9,200: 1, 9,295: 1, 9,428: 1, 9,471: 1, 9,801: 1, 9,845: 1, 10,215: 1, 10,624: 1, 10,996: 1, 11,044: 1, 11,123: 1, 11,160: 1, 11,258: 1, 11,498: 1, 11,986: 1, 12,252: 1, 12,651: 1, 12,967: 1, 13,256: 1, 13,924: 1, 14,299: 1, 14,737: 1, 15,014: 1, 15,212: 1, 16,266: 1, 17,731: 1, 19,368: 1, 19,614: 1, 19,747: 1, 20,130: 1, 20,856: 1, 22,326: 1, 22,627: 1, 23,289: 1, 23,431: 1, 23,724: 1, 24,190: 1, 24,214: 1, 24,361: 1, 24,435: 1, 24,814: 1, 25,129: 1, 25,852: 1, 26,357: 1, 27,417: 1, 29,525: 1, 29,980: 1, 33,062: 1, 33,938: 1, 34,328: 1, 35,796: 1, 37,204: 1, 47,882: 1, 53,968: 1, 55,183: 1, 56,908: 1, 61,723: 1, 71,283: 1, 75,217: 1

custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff 563: 2, 597: 1, 999: 3

----------------------

Tool: VEP
Section: General Statistics
Section help text: Table showing general statistics of VEP annotation run
Title: VEP General Statistics

Plot type: violin plot

Number of samples: 12

Metrics:
Overlapped regulatory features - Overlapped regulatory features
Overlapped transcripts - Overlapped transcripts
Overlapped genes - Overlapped genes
Existing variants - Existing variants
Novel variants - Novel variants
Variants filtered out - Variants filtered out
Variants processed - Variants processed
Lines of input read - Lines of input read

|Sample Name|Overlapped regulatory features|Overlapped transcripts|Overlapped genes|Existing variants|Novel variants|Variants filtered out|Variants processed|Lines of input read|
|---|---|---|---|---|---|---|---|---|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann|16|201|193|354|0|0|354|354|
|HCC1395_BL_custom.ann_snpEff_VEP.ann|1|6|6|3|0|0|3|4|
|HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann|0|4|4|3|0|0|3|3|
|HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann|0|2|2|2|0|0|2|2|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|5|51|51|42|0|0|42|42|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|15|169|162|300|0|0|300|300|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann|16|199|192|395|0|0|395|395|
|Sig_18_Blood_custom.ann_snpEff_VEP.ann|1|6|6|3|0|0|3|4|
|custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff_VEP.ann|0|10|10|6|0|0|6|6|
|custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff_VEP.ann|0|0|0|||0|0|0|
|custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|6|81|81|88|0|0|88|88|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|11|154|151|237|0|0|237|237|

----------------------

Tool: VEP
Section: Variant classes
Section description: Classes of variants found in the data.
Title: VEP: Variant classes

Plot type: bar plot
Values: Number of variants

|Sample|insertion|deletion|SNV|copy_number_variation|indel|chromosome_breakpoint|
|---|---|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|nan|nan|237|nan|nan|nan|
|custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|36|52|nan|nan|nan|nan|
|custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff_VEP.ann|1|2|nan|nan|1|2|
|Sig_18_Blood_custom.ann_snpEff_VEP.ann|nan|2|nan|1|nan|nan|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann|12|14|369|nan|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|nan|nan|300|nan|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|19|23|nan|nan|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|2|
|HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|1|2|
|HCC1395_BL_custom.ann_snpEff_VEP.ann|nan|2|nan|1|nan|nan|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann|9|11|334|nan|nan|nan|

----------------------

Tool: VEP
Section: Consequences
Section description: Predicted consequences of variations.
Title: VEP: Variant Consequences

Plot type: bar plot
Values: Consequences (most severe)

### Consequences (most severe)

|Sample|stop_gained|frameshift_variant|stop_lost|inframe_insertion|inframe_deletion|missense_variant|splice_region_variant|synonymous_variant|5_prime_UTR_variant|3_prime_UTR_variant|non_coding_transcript_exon_variant|intron_variant|intergenic_variant|transcript_ablation|feature_truncation|splice_acceptor_variant|splice_polypyrimidine_tract_variant|splice_donor_variant|splice_donor_5th_base_variant|splice_donor_region_variant|upstream_gene_variant|
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|2|nan|nan|nan|nan|53|3|23|5|11|11|113|1|nan|nan|nan|8|nan|2|4|1|
|custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|nan|8|nan|2|4|nan|3|nan|1|3|5|52|nan|nan|nan|1|9|nan|nan|nan|nan|
|custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|1|nan|nan|nan|nan|nan|nan|2|nan|nan|2|nan|nan|1|nan|nan|nan|
|Sig_18_Blood_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|2|nan|1|nan|nan|nan|nan|nan|nan|nan|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann|2|7|1|3|3|150|4|128|8|15|9|64|1|nan|nan|nan|nan|nan|nan|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|2|nan|1|nan|nan|62|5|32|6|12|23|140|1|nan|nan|1|8|1|4|2|nan|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|nan|nan|nan|1|5|nan|1|nan|2|2|nan|25|nan|nan|nan|1|5|nan|nan|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|2|nan|nan|nan|nan|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|1|nan|nan|2|nan|nan|nan|nan|nan|nan|
|HCC1395_BL_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|2|nan|1|nan|nan|nan|nan|nan|nan|nan|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann|1|5|1|3|2|139|2|125|9|7|7|51|2|nan|nan|nan|nan|nan|nan|nan|nan|

### Coding consequences

|Sample|stop_gained|frameshift_variant|inframe_insertion|inframe_deletion|missense_variant|synonymous_variant|stop_lost|coding_sequence_variant|
|---|---|---|---|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|2|nan|nan|nan|47|23|nan|nan|
|custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|nan|8|2|4|nan|nan|nan|nan|
|Sig_18_Blood_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|1|1|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann|2|7|2|3|140|131|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|1|nan|nan|nan|56|32|1|nan|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|nan|nan|1|4|nan|nan|nan|nan|
|HCC1395_BL_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|1|1|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann|1|5|2|2|128|127|nan|nan|

### Consequences (all)

|Sample|stop_gained|frameshift_variant|inframe_insertion|inframe_deletion|missense_variant|splice_region_variant|synonymous_variant|5_prime_UTR_variant|3_prime_UTR_variant|non_coding_transcript_exon_variant|intron_variant|non_coding_transcript_variant|upstream_gene_variant|downstream_gene_variant|regulatory_region_variant|intergenic_variant|stop_lost|feature_truncation|coding_sequence_variant|NMD_transcript_variant|splice_polypyrimidine_tract_variant|splice_acceptor_variant|splice_donor_variant|splice_donor_5th_base_variant|splice_donor_region_variant|
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|2|nan|nan|nan|47|5|23|5|10|3|195|32|50|43|18|1|nan|nan|nan|nan|11|nan|nan|2|4|
|custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|nan|8|2|4|nan|3|nan|nan|2|2|75|7|14|13|6|nan|nan|nan|nan|1|12|nan|nan|nan|nan|
|custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|nan|1|1|nan|7|1|3|1|nan|nan|nan|3|nan|nan|nan|nan|1|1|nan|
|Sig_18_Blood_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|nan|1|1|1|4|nan|nan|1|1|nan|1|2|1|1|nan|nan|nan|nan|nan|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann|2|7|2|3|140|6|131|4|14|18|153|31|73|47|28|1|nan|nan|nan|nan|nan|nan|nan|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|1|nan|nan|nan|56|6|32|5|11|10|243|35|59|44|18|1|1|nan|nan|1|11|1|1|4|2|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|nan|nan|1|4|nan|1|nan|nan|2|nan|39|3|7|11|5|nan|nan|nan|nan|nan|6|nan|nan|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|nan|nan|2|nan|nan|nan|nan|2|nan|nan|nan|2|nan|nan|nan|nan|nan|nan|nan|
|HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|nan|nan|nan|nan|3|nan|2|nan|nan|nan|nan|2|nan|nan|nan|nan|nan|nan|nan|
|HCC1395_BL_custom.ann_snpEff_VEP.ann|nan|nan|nan|nan|nan|nan|nan|1|1|1|4|nan|nan|1|1|nan|1|2|1|1|nan|nan|nan|nan|nan|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann|1|5|2|2|128|4|127|3|8|16|152|37|54|62|26|2|nan|nan|nan|nan|nan|nan|nan|nan|nan|


----------------------

Tool: VEP
Section: SIFT summary
Section description: SIFT variant effect prediction.
Title: VEP: SIFT summary

Plot type: bar plot
Values: Number of variants

|Sample|Tolerated|Tolerated low confidence|Deleterious low confidence|Deleterious|
|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|16|7|9|15|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann|79|25|14|21|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|27|6|9|14|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann|70|24|11|22|

----------------------

Tool: VEP
Section: PolyPhen summary
Section description: PolyPhen variant effect prediction.
Title: VEP: PolyPhen summary

Plot type: bar plot
Values: Number of variants

|Sample|Benign|Possibly damaging|Probably damaging|Unknown|
|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|22|2|7|12|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann|93|14|9|21|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|25|5|4|17|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann|84|7|12|21|

----------------------

Tool: VEP
Section: Variants by chromosome
Section description: Number of variants found on each chromosome.
Title: VEP: Variants by chromosome

Plot type: bar plot
Values: Number of variants

|Sample|chr1|chr9|chrX|chr21|
|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|nan%|nan%|nan%|100%|
|custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|nan%|nan%|nan%|100%|
|custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff_VEP.ann|nan%|nan%|nan%|100%|
|Sig_18_Blood_custom.ann_snpEff_VEP.ann|33%|33%|33%|nan%|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann|nan%|nan%|nan%|100%|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|nan%|nan%|nan%|100%|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|nan%|nan%|nan%|100%|
|HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann|nan%|nan%|nan%|100%|
|HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann|nan%|nan%|nan%|100%|
|HCC1395_BL_custom.ann_snpEff_VEP.ann|33%|33%|33%|nan%|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann|nan%|nan%|nan%|100%|

----------------------

Tool: VEP
Section: Position in protein
Section description: Relative position of affected amino acids in protein.
Title: VEP: Position in protein

Plot type: bar plot
Values: Number of variants

|Sample|00-10%|10-20%|20-30%|30-40%|40-50%|50-60%|60-70%|70-80%|80-90%|90-100%|
|---|---|---|---|---|---|---|---|---|---|---|
|custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|8%|13%|9%|9%|2%|26%|8%|11%|4%|5%|
|custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|21%|7%|0%|14%|7%|21%|0%|7%|7%|14%|
|Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann|9%|11%|8%|10%|9%|10%|8%|10%|11%|9%|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann|8%|8%|10%|14%|6%|14%|13%|4%|10%|8%|
|HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann|40%|0%|0%|20%|0%|0%|0%|20%|0%|20%|
|HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann|10%|11%|8%|10%|10%|8%|9%|10%|10%|9%|

----------------------

Tool: nf-core/sarek Methods Description
Section: 
<h4>Methods</h4>
<p>Data was processed using nf-core/sarek v3.5.0  of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
<p>The pipeline was executed with Nextflow v25.10.2 (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
<pre><code>nextflow run 'https://gitlab.natera.com/rd-platform/bioinformatics/nextflow/sarek.git' 'https://gitlab.natera.com/rd-platform/bioinformatics/nextflow/sarek.git' -name gitlab-sarek-build2797494-baseline-run-63551853 -r 0a8d591cb5d0b9e8f429661846c0d6fec2347eaf -profile docker,test_regression,eks --outdir 's3://natera-rnd-pltf-dev-s3-gitlab-results/sarek/build2797494/baseline-run/63551853' -output-dir 's3://natera-rnd-pltf-dev-s3-gitlab-results/sarek/build2797494/baseline-run/63551853'</code></pre>
<p></p>
<h4>References</h4>
<ul>
  <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
  <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
  <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
  <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
  
</ul>
<div class="alert alert-info">
  <h5>Notes:</h5>
  <ul>
    <li>If available, make sure to update the text to include the Zenodo DOI of the pipeline version used. </li>
    <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
    <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
  </ul>
</div>