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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.25.1

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        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.

        Report generated on 2026-01-26, 01:56 UTC based on data in: /tmp/nxf.MnBDC0ECpP

        General Statistics

        Showing 0/18 rows and 7/10 columns.
        Sample NameVarsSNPIndelTs/TvMNPMultiallelicMultiallelic SNPChange rateTs/TvM Variants
        1029_BGFD-N1-BDNA-1_2375WFLT3_s30.entropy.entropy
        637
        0
        0
        0.00
        0
        0
        0
        1029_BGFD-N1-BDNA-1_2375WFLT3_s30.entropy.entropy_custom.ann_snpEff
        4758308
        0.000
        0.00M
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.manta.diploid_sv
        112
        0
        63
        0.00
        0
        0
        0
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.manta.diploid_sv_custom.ann_snpEff
        26002149
        0.000
        0.00M
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.manta.somatic_sv
        85
        0
        1
        0.00
        0
        0
        0
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.manta.somatic_sv_custom.ann_snpEff
        31863974
        0.000
        0.00M
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.filtered
        13643
        8834
        4571
        2.86
        782
        1688
        101
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.filtered_custom.ann_snpEff
        175310
        3.084
        0.02M
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.whatshap
        13643
        8834
        4571
        2.86
        782
        1688
        101
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.whatshap.phased_custom.ann_snpEff
        175310
        3.084
        0.02M
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.strelka.somatic_indels
        2279
        0
        2279
        0.00
        0
        0
        0
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.strelka.somatic_indels_custom.ann_snpEff
        1329987
        0.000
        0.00M
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.strelka.somatic_snvs
        15424
        15424
        0
        2.55
        0
        0
        0
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.strelka.somatic_snvs_custom.ann_snpEff
        200224
        2.547
        0.02M
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.tiddit_sv_merge
        805
        0
        0
        0.00
        0
        0
        0
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.tiddit_sv_merge_custom.ann_snpEff
        3836360
        0.000
        0.00M
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.tnseq.filtered
        37202
        31022
        5586
        3.05
        1231
        1946
        125
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.tnseq.filtered_custom.ann_snpEff
        74169
        3.130
        0.04M

        Bcftools

        Utilities for variant calling and manipulating VCFs and BCFs.URL: https://samtools.github.io/bcftoolsDOI: 10.1093/gigascience/giab008

        Variant Substitution Types

        Created with MultiQC

        Variant Quality

        Created with MultiQC

        Indel Distribution

        Created with MultiQC

        Variant depths

        Read depth support distribution for called variants

        Created with MultiQC

        Vcftools

        Program to analyse and reporting on VCF files.URL: https://vcftools.github.ioDOI: 10.1093/bioinformatics/btr330

        TsTv by Count

        Plot of TSTV-BY-COUNT - the transition to transversion ratio as a function of alternative allele count from the output of vcftools TsTv-by-count.

        Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Alternative allele count 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 --TsTv-by-count

        Created with MultiQC

        TsTv by Qual

        Plot of TSTV-BY-QUAL - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.

        Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Quality 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 --TsTv-by-qual

        Created with MultiQC

        SNPeff

        Annotates and predicts the effects of variants on genes (such as amino acid changes).URL: http://snpeff.sourceforge.netDOI: 10.4161/fly.19695

        Variants by Genomic Region

        The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.

        The upstream and downstream interval size to detect these genomic regions is 5000bp by default.

        Created with MultiQC

        Variant Effects by Impact

        The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.

        There are four levels of impacts predicted by SnpEff:

        • High: High impact (like stop codon)
        • Moderate: Middle impact (like same type of amino acid substitution)
        • Low: Low impact (ie silence mutation)
        • Modifier: No impact
        Created with MultiQC

        Variants by Effect Types

        The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.

        This plot shows the effect of variants with respect to the mRNA.

        Created with MultiQC

        Variants by Functional Class

        The stacked bar plot shows the effect of variants and the number of variants for each effect type.

        This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:

        • Silent: The amino acid does not change.
        • Missense: The amino acid is different.
        • Nonsense: The variant generates a stop codon.
        Created with MultiQC

        Variant Qualities

        The line plot shows the quantity as function of the variant quality score.

        The quality score corresponds to the QUAL column of the VCF file. This score is set by the variant caller.

        Created with MultiQC

        VEP

        Determines the effect of variants on genes, transcripts and protein sequences, as well as regulatory regions.URL: https://www.ensembl.org/info/docs/tools/vep/index.htmlDOI: 10.1186/s13059-016-0974-4

        General Statistics

        Table showing general statistics of VEP annotation run

        Showing 0/9 rows and 7/8 columns.
        Sample NameOverlapped regulatory featuresOverlapped transcriptsOverlapped genesExisting variantsNovel variantsVariants filtered outVariants processedLines of input read
        1029_BGFD-N1-BDNA-1_2375WFLT3_s30.entropy.entropy_custom.ann_snpEff_VEP.ann
        2279
        1412
        1402
        637
        0
        0
        637
        637
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.manta.diploid_sv_custom.ann_snpEff_VEP.ann
        44
        142
        142
        112
        0
        0
        112
        112
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.manta.somatic_sv_custom.ann_snpEff_VEP.ann
        3
        65
        65
        84
        0
        0
        84
        85
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.filtered_custom.ann_snpEff_VEP.ann
        336
        6989
        6880
        13643
        0
        0
        13643
        13643
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann
        336
        6989
        6880
        13643
        0
        0
        13643
        13643
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.strelka.somatic_indels_custom.ann_snpEff_VEP.ann
        168
        3167
        3147
        2279
        0
        0
        2279
        2279
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann
        378
        12358
        12081
        15424
        0
        0
        15424
        15424
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.tiddit_sv_merge_custom.ann_snpEff_VEP.ann
        2681
        1798
        1787
        803
        0
        0
        803
        805
        1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30.tnseq.filtered_custom.ann_snpEff_VEP.ann
        945
        18183
        17568
        37202
        0
        0
        37202
        37202

        Variant classes

        Classes of variants found in the data.

        Created with MultiQC

        Consequences

        Predicted consequences of variations.

        Created with MultiQC

        SIFT summary

        SIFT variant effect prediction.

        Created with MultiQC

        PolyPhen summary

        PolyPhen variant effect prediction.

        Created with MultiQC

        Variants by chromosome

        Number of variants found on each chromosome.

        Created with MultiQC

        Position in protein

        Relative position of affected amino acids in protein.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        AGGREGATE_VARIANT_QCaggregate_qc_metrics1.0.0
        python3.12.6
        ASCATalleleCounter4.3.0
        ascat3.1.1
        BCFTOOLS_ANNOTATEbcftools1.2
        BCFTOOLS_QUERYbcftools1.22
        BCFTOOLS_STATSbcftools1.2
        CALCULATECONTAMINATIONgatk44.5.0.0
        CNNSCOREVARIANTSgatk44.5.0.0
        CNVKIT_BATCHcnvkit0.9.10
        CNVKIT_CALLcnvkit0.9.10
        CNVKIT_EXPORTcnvkit0.9.10
        CNVKIT_GENEMETRICScnvkit0.9.10
        CNV_FACETSfacets0.6.2
        CONPAIR_CONTAMINATIONconpair1.0
        numpy1.24.4
        python3.8.20
        CONPAIR_PILEUPconpair1.0
        gatk4.6.2.0 Using
        python3.8.20
        CRAM_FILTER_HLAsambambanull
        samtools1.23
        ENSEMBLVEP_VEPensemblvep113.0
        FILTERMUTECTCALLSgatk44.5.0.0
        FILTERVARIANTTRANCHESgatk44.5.0.0
        GATHERPILEUPSUMMARIES_NORMALgatk44.5.0.0
        GATHERPILEUPSUMMARIES_TUMORgatk44.5.0.0
        GATK4_HAPLOTYPECALLERgatk44.5.0.0
        GETPILEUPSUMMARIES_NORMALgatk44.5.0.0
        GETPILEUPSUMMARIES_TUMORgatk44.5.0.0
        HLA_CONVERT_OPTITYPEhla_to_json_vcf1.0.0
        python3.13.11
        INDEL_ENTROPY_ANNOTATIONnumpy2.4.0
        pysam0.23.3
        python3.13.11
        scipy1.16.3
        LEARNREADORIENTATIONMODELgatk44.5.0.0
        MANTA_GERMLINEmanta1.6.0
        MANTA_SOMATICmanta1.6.0
        MERGEMUTECTSTATSgatk44.5.0.0
        MERGE_HAPLOTYPECALLERgatk44.5.0.0
        MERGE_MUTECT2gatk44.5.0.0
        MERGE_SENTIEON_HAPLOTYPER_VCFSgatk44.5.0.0
        MERGE_STRELKAgatk44.5.0.0
        MERGE_STRELKA_GENOMEgatk44.5.0.0
        MERGE_STRELKA_INDELSgatk44.5.0.0
        MERGE_STRELKA_SNVSgatk44.5.0.0
        MSISENSOR2_MSImsisensor20.1
        MSISENSORPRO_MSISOMATICmsisensor-pro1.2.0
        MUTECT2_PAIREDgatk44.5.0.0
        OPTITYPEoptitype1.3.1
        SAMTOOLS_MPILEUPsamtools1.21
        SCARHRDscarHRD0.6.2
        SENTIEON_HAPLOTYPERsentieon202308.03
        SENTIEON_TNFILTERsentieon202308.03
        SENTIEON_TNHAPLOTYPER2sentieon202308.03
        SNPEFF_SNPEFFsnpeff5.1d
        STRELKA_SINGLEstrelka2.9.10
        STRELKA_SOMATICstrelka2.9.10
        SVDB_MERGEbcftools1.21
        svdb2.8.2
        TABIX_BGZIPTABIXtabix1.2
        TABIX_BGZIP_TIDDIT_SVtabix1.2
        TABIX_TABIXtabix1.2
        TABIX_VCF_FOR_ENTROPYtabix1.2
        TIDDIT_SVtiddit3.6.1
        TIH_HRD_CALLINGhrd_calling0.2.0
        r-base4.3.3
        VCFTOOLS_TSTV_COUNTvcftools0.1.16
        WHATSHAP_MUTECT2whatshap2.8
        WorkflowNextflow25.10.2
        nf-core/sarekv3.5.0

        nf-core/sarek Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/sarek

        Methods

        Data was processed using nf-core/sarek v3.5.0 (doi: 10.12688/f1000research.16665.2), (doi: 10.1093/nargab/lqae031), (doi: 10.5281/zenodo.3476425) 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 /code/main.nf -profile eks,docker,std_run --input samplesheet_1029_BGFD.csv --outdir 's3://natera-platform-sandbox/users/abshah/sarek/outputs/test_1029_BGFD-variants-3' --step variant_calling --genome GATK.GRCh38 --tools sentieon_dedup,ngscheckmate,contamination,mutect2,tnseq,strelka,manta,tiddit,msisensorpro,msisensor2,ascat,cnvkit,facets,hla_optitype,tmb,hrd,whatshap,snpeff,merge,sentieon_haplotyper,haplotypecaller,indelentropy --wes true --save_output_as_bam true -params-file 1029_BGFD-params.json -name sarek-1029_BGFD-variants-3

        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:
        • 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.

        nf-core/sarek Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/sarek

        Input/output options

        input
        samplesheet_1029_BGFD.csv
        outdir
        s3://natera-platform-sandbox/users/abshah/sarek/outputs/test_1029_BGFD-variants-3
        step
        variant_calling

        Main options

        intervals
        s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed
        nucleotides_per_second
        20000
        tools
        sentieon_dedup,ngscheckmate,contamination,mutect2,tnseq,strelka,manta,tiddit,msisensorpro,msisensor2,ascat,cnvkit,facets,hla_optitype,tmb,hrd,whatshap,snpeff,merge,sentieon_haplotyper,haplotypecaller,indelentropy
        wes
        true

        Preprocessing

        aligner
        sentieon-bwamem
        save_output_as_bam
        true

        Variant Calling

        cf_chrom_len
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len
        pon
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/PON/aih_blood_normal_36_pon.vcf.gz
        pon_tbi
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/PON/aih_blood_normal_36_pon.vcf.gz.tbi

        General reference genome options

        hlala_graph
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/HLA_LA/PRG_MHC_GRCh38_withIMGT_indexed/
        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/
        xhla_chr6_bwa
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/xHLA/Sequence/BWAIndex/
        xhla_chr6_fai
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/xHLA/Sequence/chr6/hg38.chr6.fasta.fai
        xhla_chr6_fasta
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/xHLA/Sequence/chr6/hg38.chr6.fasta
        yara
        s3://natera-platform-sandbox/pipeline-resources/AIH/hla_typing/hla_index/

        Reference genome options

        ascat_alleles
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip
        ascat_genome
        hg38
        ascat_loci
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip
        ascat_loci_gc
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip
        ascat_loci_rt
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip
        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
        bwa
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/
        bwamem2
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/
        chr_dir
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes
        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
        community.wave.seqera.io
        contam_bed
        s3://natera-platform-sandbox/platform-users/ralla/nfcore_rnafusion_resources/GRCh38/gatk4/dbsnp_hg38_contam_sites.bed
        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
        dragmap
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/dragmap/
        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_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
        known_indels
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz
        known_indels_tbi
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi
        known_indels_vqsr
        --resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
        known_snps
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz
        known_snps_tbi
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi
        known_snps_vqsr
        --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz
        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
        mappability
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem
        ngscheckmate_bed
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed
        ngscheckmate_fastq_pt
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.pt
        probe_bed
        s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38.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
        sentieon_dnascope_model
        s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
        seqtool_dbsnp
        s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz
        seqtool_dbsnp_index
        s3://natera-platform-sandbox/pipeline-resources/Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
        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/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.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/xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_footprint.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38.bed,s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/FINAL_hotspot_list_07302025_hg38_sorted.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/

        Generic options

        task_job_queue
        Nextflow-OnDemand

        Core Nextflow options

        configFiles
        N/A
        containerEngine
        docker
        launchDir
        /code
        profile
        eks,docker,std_run
        projectDir
        /code
        runName
        sarek-1029_BGFD-variants-3
        userName
        nextflow
        workDir
        /natera-rnd-pltf-dev-nextflow-scratch-01/work

        MultiQC v1.25.1 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.