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        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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        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 2026-02-02, 23:55 UTC based on data in: /tmp/nxf.ZwRfrp8O39

        General Statistics

        Showing 0/36 rows and 7/10 columns.
        Sample NameVarsSNPIndelTs/TvMNPMultiallelicMultiallelic SNPChange rateTs/TvM Variants
        1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.entropy.entropy
        1298
        0
        0
        0.00
        0
        0
        0
        1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.entropy.entropy_custom.ann_snpEff
        23233615
        0.000
        0.00M
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.manta.diploid_sv
        133
        0
        67
        0.00
        0
        0
        0
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.manta.diploid_sv_custom.ann_snpEff
        22201730
        0.000
        0.00M
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.manta.somatic_sv
        47
        0
        3
        0.00
        0
        0
        0
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.manta.somatic_sv_custom.ann_snpEff
        43483596
        0.000
        0.00M
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.mutect2.filtered
        4368
        3704
        581
        5.00
        96
        72
        2
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.mutect2.filtered_custom.ann_snpEff
        677933
        5.057
        0.00M
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.mutect2.whatshap
        4368
        3704
        581
        5.00
        96
        72
        2
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.mutect2.whatshap.phased_custom.ann_snpEff
        677933
        5.057
        0.00M
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.strelka.somatic_indels
        1509
        0
        1509
        0.00
        0
        0
        0
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.strelka.somatic_indels_custom.ann_snpEff
        2008643
        0.000
        0.00M
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.strelka.somatic_snvs
        26633
        26633
        0
        3.47
        0
        0
        0
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.strelka.somatic_snvs_custom.ann_snpEff
        113807
        3.466
        0.03M
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.tiddit_sv_merge
        1075
        0
        0
        0.00
        0
        0
        0
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.tiddit_sv_merge_custom.ann_snpEff
        2872809
        0.000
        0.00M
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.tnseq.filtered
        25226
        23603
        1227
        3.22
        443
        189
        16
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.tnseq.filtered_custom.ann_snpEff
        118985
        3.228
        0.03M
        1029_BG5-N1-BDNA-1_2375WFLT3_s29.entropy.entropy
        1472
        0
        0
        0.00
        0
        0
        0
        1029_BG5-N1-BDNA-1_2375WFLT3_s29.entropy.entropy_custom.ann_snpEff
        2098009
        0.000
        0.00M
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.manta.diploid_sv
        131
        0
        63
        0.00
        0
        0
        0
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.manta.diploid_sv_custom.ann_snpEff
        23866475
        0.000
        0.00M
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.manta.somatic_sv
        20
        0
        0
        0.00
        0
        0
        0
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.manta.somatic_sv_custom.ann_snpEff
        51346729
        0.000
        0.00M
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.mutect2.filtered
        1060
        801
        217
        1.94
        47
        24
        1
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.mutect2.filtered_custom.ann_snpEff
        2778224
        1.955
        0.00M
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.mutect2.whatshap
        1060
        801
        217
        1.94
        47
        24
        1
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.mutect2.whatshap.phased_custom.ann_snpEff
        2778224
        1.955
        0.00M
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.strelka.somatic_indels
        2533
        0
        2533
        0.00
        0
        0
        0
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.strelka.somatic_indels_custom.ann_snpEff
        1219214
        0.000
        0.00M
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.strelka.somatic_snvs
        27128
        27128
        0
        1.97
        0
        0
        0
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.strelka.somatic_snvs_custom.ann_snpEff
        113840
        1.972
        0.03M
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.tiddit_sv_merge
        1218
        0
        0
        0.00
        0
        0
        0
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.tiddit_sv_merge_custom.ann_snpEff
        2535525
        0.000
        0.00M
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.tnseq.filtered
        21824
        20675
        784
        2.94
        406
        123
        19
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.tnseq.filtered_custom.ann_snpEff
        137981
        2.955
        0.02M

        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 0/18 rows and 7/8 columns.
        Sample NameOverlapped regulatory featuresOverlapped transcriptsOverlapped genesExisting variantsNovel variantsVariants filtered outVariants processedLines of input read
        1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.entropy.entropy_custom.ann_snpEff_VEP.ann
        985
        17324
        16716
        29380
        0
        0
        29380
        29380
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.manta.diploid_sv_custom.ann_snpEff_VEP.ann
        56
        203
        203
        133
        0
        0
        133
        133
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.manta.somatic_sv_custom.ann_snpEff_VEP.ann
        3
        47
        47
        47
        0
        0
        47
        47
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.mutect2.filtered_custom.ann_snpEff_VEP.ann
        155
        5141
        5100
        4368
        0
        0
        4368
        4368
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann
        155
        5141
        5100
        4368
        0
        0
        4368
        4368
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.strelka.somatic_indels_custom.ann_snpEff_VEP.ann
        65
        1525
        1507
        1509
        0
        0
        1509
        1509
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann
        666
        17616
        17026
        26633
        0
        0
        26633
        26633
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.tiddit_sv_merge_custom.ann_snpEff_VEP.ann
        7051
        2230
        2219
        1059
        0
        0
        1059
        1075
        1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.tnseq.filtered_custom.ann_snpEff_VEP.ann
        767
        17102
        16546
        25226
        0
        0
        25226
        25226
        1029_BG5-N1-BDNA-1_2375WFLT3_s29.entropy.entropy_custom.ann_snpEff_VEP.ann
        36
        176
        176
        127
        0
        0
        127
        127
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.manta.diploid_sv_custom.ann_snpEff_VEP.ann
        36
        171
        171
        131
        0
        0
        131
        131
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.manta.somatic_sv_custom.ann_snpEff_VEP.ann
        1
        13
        13
        20
        0
        0
        20
        20
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.mutect2.filtered_custom.ann_snpEff_VEP.ann
        28
        1171
        1167
        1060
        0
        0
        1060
        1060
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.mutect2.whatshap.phased_custom.ann_snpEff_VEP.ann
        28
        1171
        1167
        1060
        0
        0
        1060
        1060
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.strelka.somatic_indels_custom.ann_snpEff_VEP.ann
        187
        2774
        2748
        2533
        0
        0
        2533
        2533
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann
        875
        19371
        18709
        27128
        0
        0
        27128
        27128
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.tiddit_sv_merge_custom.ann_snpEff_VEP.ann
        4358
        1676
        1664
        1199
        0
        0
        1199
        1218
        1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29.tnseq.filtered_custom.ann_snpEff_VEP.ann
        660
        15366
        14903
        21824
        0
        0
        21824
        21824

        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
        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
        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
        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-gb019307

        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 'https://gitlab.natera.com/rd-platform/bioinformatics/nextflow/sarek.git' -output-dir 's3://natera-rnd-pltf-dev-nextflow-data-01/users/mipeters/semiproductionize/sarek/69812fed/test_regression_recal_dev_b0193075' -r b01930759a3b33240c8606994ac2e827477e9263 -profile docker,eks,test_regression --input 's3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp-dna-abtest/samplesheets/samplesheet_sarek_A2375WFLT3_B23FC2GLT4_recal_bams_from_daq_smallest2_tn_pairs.csv' --step variant_calling --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' --exome_bed 's3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed' --outdir 's3://natera-rnd-pltf-dev-nextflow-data-01/users/mipeters/semiproductionize/sarek/69812fed/test_regression_recal_dev_b0193075' -name mipeters-regression-recal-dev-69812fed

        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
        s3://natera-platform-sandbox/platform-infra/stories/PLTFINF-169-semiproductionize/cgp-dna-abtest/samplesheets/samplesheet_sarek_A2375WFLT3_B23FC2GLT4_recal_bams_from_daq_smallest2_tn_pairs.csv
        outdir
        s3://natera-rnd-pltf-dev-nextflow-data-01/users/mipeters/semiproductionize/sarek/69812fed/test_regression_recal_dev_b0193075
        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
        500
        tools
        sentieon_dedup,ngscheckmate,contamination,mutect2,tnseq,strelka,manta,tiddit,msisensorpro,msisensor2,ascat,cnvkit,facets,tmb,hrd,whatshap,snpeff,merge,sentieon_haplotyper,haplotypecaller,chip_detection,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
        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
        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
        292967571998.dkr.ecr.us-west-2.amazonaws.com/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-inputs/test_sarek/end_to_end_regression/bed/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_chr21.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-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
        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
        docker,eks,test_regression
        projectDir
        /tmp/home/.nextflow/assets/rd-platform/bioinformatics/nextflow/sarek
        runName
        mipeters-regression-recal-dev-69812fed
        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.