A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the documentation.
/tmp/nxf.nzyqi368Gd
General Statistics
Showing 786 samples.
altera/sarek Workflow Summary
- this information is collected when the pipeline is started.https://github.com/altera/sarek
Input/output options
- input
- s3://natera-platform-sandbox/platform-users/mohsen/msi/mimsi_outputs/samplesheet_mimsi_low_input_remaining.csv
- outdir
- s3://natera-platform-sandbox/platform-users/mohsen/msi/mimsi_outputs/mimsi_run__20260603-232548
Main options
- hrd_coverage_profile
- s3://natera-platform-sandbox/pipeline-resources/AIH/hrd_score_altera_bam/dbsnp_baseline_altera.260120.tsv.gz
- intervals_dir
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals
- intervals_vc_dir
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_padded_intervals
- mimsi_microsatellites_list
- s3://natera-platform-sandbox/pipeline-resources/mimsi/1500_dropped_panel_with_boosted_msi_regions.tsv
- mimsi_model
- s3://natera-platform-sandbox/pipeline-resources/mimsi/mi_msi_v0_4_0_200x_attn.model
- tools
- mimsi
- wes
- true
Variant Calling
- chip_cohort_blacklist
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cohort_blacklist.bed.gz
- chip_cosmic_heme
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cosmic_heme.tsv.gz
- chip_encode_blacklist
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/encode_blacklist.bed.gz
- chip_gene_family_blacklist
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_family_blacklist.bed.gz
- chip_gene_tiers
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_tiers.tsv
- chip_pon
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP_PON/pon.hotspot_protected.raw.vcf.gz
- chip_pon_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CHIP_PON/pon.hotspot_protected.raw.vcf.gz.tbi
- cnvkit_reference
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/cnvkit/cnvkit_wes_altera.reference.cnn
- pon
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz
- pon_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz.tbi
General reference genome options
- igenomes_base
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/
- optitype_reference
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/optitype/original_v3.15_2014/
Reference genome options
- blacklist_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/blacklist_grch38.bed.gz
- blacklist_bed_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/blacklist_grch38.bed.gz.tbi
- blacklist_header
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/blacklist_header.txt
- conpair_markers
- 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
- container_registry_seqera
- 292967571998.dkr.ecr.us-west-2.amazonaws.com/community.wave.seqera.io
- dbsnp
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
- dbsnp_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
- dbsnp_vqsr
- --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
- dict
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
- exome_bed
- s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed
- fasta
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
- fasta_fai
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
- genome_annotations
- s3://natera-platform-sandbox/pipeline-resources/ensembl/Homo_sapiens.GRCh38.110.gtf.gz
- germline_rescue_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/germline_rescue_targets.bed
- germline_resource
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
- germline_resource_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
- gt_correction_model
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/gt_correction_model_v2.joblib
- gt_correction_threshold_grch38
- 0.5
- lowdepth_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_grch38.tsv.gz
- lowdepth_bed_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_grch38.tsv.gz.tbi
- lowdepth_header
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_header.txt
- ngscheckmate_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed
- probe_bed
- s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
- repeatmasker_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_grch38.bed.gz
- repeatmasker_bed_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_grch38.bed.gz.tbi
- repeatmasker_header
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_header.txt
- rf_blacklist_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_blacklist.bed.gz
- rf_blacklist_bed_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_blacklist.bed.gz.tbi
- rf_boosted_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_boosted_exons.bed.gz
- rf_boosted_bed_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_boosted_exons.bed.gz.tbi
- rf_indel_fp_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_fp_regions.bed.gz
- rf_indel_fp_bed_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_fp_regions.bed.gz.tbi
- rf_indel_fp_rates_tsv
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_locus_fp_rates.tsv
- rf_indel_model
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_rf_model_v7.joblib
- rf_low_depth_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_low_depth.bed.gz
- rf_low_depth_bed_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_low_depth.bed.gz.tbi
- rf_repeatmasker_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz
- rf_repeatmasker_bed_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz.tbi
- rf_snv_fp_bed
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_fp_regions.bed.gz
- rf_snv_fp_bed_tbi
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_fp_regions.bed.gz.tbi
- rf_snv_model
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_rf_model_v4.joblib
- snpeff_cache
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/annotation-cache/snpeff_cache/
- snpeff_db
- GRCh38.105
- target_beds
- s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_coding_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/altera_v3_targets_noncoding_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/FINAL_hotspot_list_07302025_hg38_sorted.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/foresight_clarity_targets_hg38.bed
- vep_cache
- s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/annotation-cache/vep_cache/
- vep_cache_version
- 113
- vep_genome
- GRCh38
- vep_species
- homo_sapiens
Institutional config options
- modules_testdata_base_path
- s3://natera-platform-sandbox/pipeline-inputs/test_sarek/
Low reads filtering
- min_mapped_reads_normal
- 25000000
- min_mapped_reads_tumor
- 50000000
Generic options
- task_job_queue
- Nextflow-OnDemand
Core Nextflow options
- configFiles
- N/A
- container
- [GERMLINE_CNV:292967571998.dkr.ecr.us-west-2.amazonaws.com/sarek/altera_cnv:0.5.0]
- containerEngine
- docker
- launchDir
- /code
- profile
- docker,std_run,eks,slack
- projectDir
- /tmp/home/.nextflow/assets/rd-platform/bioinformatics/nextflow/sarek
- runName
- mimsi-low-input-remaining-20260603-232548
- userName
- nextflow
- workDir
- /natera-rnd-pltf-dev-nextflow-scratch-01/work
Samtools Flagstat
Toolkit for interacting with BAM/CRAM files.http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352
Percent mapped
Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.
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.
Alignment stats
This module parses the output from samtools stats. All numbers in millions.
Showing 786 samples.
Mosdepth
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.https://github.com/brentp/mosdepthDOI: 10.1093/bioinformatics/btx699
Cumulative coverage distribution
Proportion of bases in the reference genome with, at least, a given depth of coverage. Note that for 786 samples, a BED file was provided, so the data was calculated across those regions. For 786 samples, it's calculated across the entire genome length. 786 samples have both global and region reports, and we are showing the data for regions
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 (Sims et al. 2014).
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 (Sims et al. 2014), 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 (Green 2007).
For increasing coverage depths (1×, 2×, …, N×), 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.
Average coverage per contig
Average coverage per contig or chromosome
XY coverage
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| AGGREGATE_VARIANT_QC | aggregate_qc_metrics | 2.0.0 |
| python | 3.12.6 | |
| MIMSI_ANALYZE | mimsi | 0.4.5.1 |
| Mosdepth | mosdepth | 0.3.8 |
| SAMTOOLS_IDXSTATS_COUNT | bai_mapped_count | 1.0.0 |
| python | 3.12.6 | |
| SAMTOOLS_STATS | samtools | 1.21 |
| VARIANT_QC_TO_CSV | python | 3.12.6 |
| variant_qc_to_csv | 1.0.0 | |
| WRITE_PURGE_REPORT | bash | 5.2.15(1)-release |
| Workflow | Nextflow | 25.10.2 |
| altera/sarek | v3.5.0-gaf44597 |
nf-core/sarek Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.https://github.com/nf-core/sarek
Methods
Data was processed using nf-core/sarek v3.5.0 of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v25.10.2 (Di Tommaso et al., 2017) with the following command:
nextflow run 'https://gitlab.natera.com/rd-platform/bioinformatics/nextflow/sarek.git' -output-dir 's3://natera-platform-sandbox/platform-users/mohsen/msi/mimsi_outputs/mimsi_run__20260603-232548' -r af445972 -name mimsi-low-input-remaining-20260603-232548 -profile docker,std_run,eks,slack --input 's3://natera-platform-sandbox/platform-users/mohsen/msi/mimsi_outputs/samplesheet_mimsi_low_input_remaining.csv' --outdir 's3://natera-platform-sandbox/platform-users/mohsen/msi/mimsi_outputs/mimsi_run__20260603-232548' --tools mimsi --mimsi_microsatellites_list 's3://natera-platform-sandbox/pipeline-resources/mimsi/1500_dropped_panel_with_boosted_msi_regions.tsv' --mimsi_model 's3://natera-platform-sandbox/pipeline-resources/mimsi/mi_msi_v0_4_0_200x_attn.model'References
- 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: 10.1038/nbt.3820
- 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: 10.1038/s41587-020-0439-x
- 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: 10.1038/s41592-018-0046-7
- 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: 10.1093/bioinformatics/btx192
Notes:
- If available, make sure to update the text to include the Zenodo DOI of the pipeline version used.
- 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!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.