├── .dockstore.yml ├── .gitignore ├── LICENSE ├── README.md ├── bin ├── compile_aln_variants_metrics.py ├── count_aln.py ├── count_variants.py └── metrics │ ├── __init__.py │ └── metrics.py ├── conf ├── awsbatch.config ├── docker.config └── resources.config ├── containers ├── Dockerfile ├── build_npm-sample-qc_docker_image.sh ├── build_npm-sample-qc_singularity_image.sh └── conda_env.yml ├── docs ├── .buildinfo ├── .nojekyll ├── _sources │ ├── api │ │ ├── metrics.count_deletions.rst.txt │ │ ├── metrics.count_insertions.rst.txt │ │ ├── metrics.count_snvs.rst.txt │ │ ├── metrics.cross_contamination_rate.rst.txt │ │ ├── metrics.insert_size_std_deviation.rst.txt │ │ ├── metrics.mad_autosome_coverage.rst.txt │ │ ├── metrics.mean_autosome_coverage.rst.txt │ │ ├── metrics.mean_insert_size.rst.txt │ │ ├── metrics.pct_autosomes_15x.rst.txt │ │ ├── metrics.pct_reads_mapped.rst.txt │ │ ├── metrics.pct_reads_properly_paired.rst.txt │ │ ├── metrics.ratio_heterozygous_homzygous_indel.rst.txt │ │ ├── metrics.ratio_heterozygous_homzygous_snv.rst.txt │ │ ├── metrics.ratio_insertion_deletion.rst.txt │ │ ├── metrics.ratio_transitions_transversions.rst.txt │ │ ├── metrics.rst.txt │ │ └── metrics.yield_bp_q30.rst.txt │ ├── index.rst.txt │ └── metrics.rst.txt ├── _static │ ├── _sphinx_javascript_frameworks_compat.js │ ├── basic.css │ ├── css │ │ ├── badge_only.css │ │ ├── fonts │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ ├── fontawesome-webfont.woff2 │ │ │ ├── lato-bold-italic.woff │ │ │ ├── lato-bold-italic.woff2 │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-normal-italic.woff │ │ │ ├── lato-normal-italic.woff2 │ │ │ ├── lato-normal.woff │ │ │ └── lato-normal.woff2 │ │ └── theme.css │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── fonts │ │ ├── Lato-Bold.ttf │ │ ├── Lato-Bold.woff2 │ │ ├── Lato-BoldItalic.ttf │ │ ├── Lato-BoldItalic.woff2 │ │ ├── Lato-Italic.ttf │ │ ├── Lato-Italic.woff2 │ │ ├── Lato-Regular.ttf │ │ ├── Lato-Regular.woff2 │ │ ├── Lato │ │ │ ├── lato-bold.eot │ │ │ ├── lato-bold.ttf │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-bolditalic.eot │ │ │ ├── lato-bolditalic.ttf │ │ │ ├── lato-bolditalic.woff │ │ │ ├── lato-bolditalic.woff2 │ │ │ ├── lato-italic.eot │ │ │ ├── lato-italic.ttf │ │ │ ├── lato-italic.woff │ │ │ ├── lato-italic.woff2 │ │ │ ├── lato-regular.eot │ │ │ ├── lato-regular.ttf │ │ │ ├── lato-regular.woff │ │ │ └── lato-regular.woff2 │ │ ├── RobotoSlab-Bold.woff2 │ │ ├── RobotoSlab-Regular.woff2 │ │ ├── RobotoSlab │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ └── roboto-slab-v7-regular.woff2 │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ └── fontawesome-webfont.woff2 │ ├── graphviz.css │ ├── jquery-3.6.0.js │ ├── jquery.js │ ├── js │ │ ├── badge_only.js │ │ ├── html5shiv-printshiv.min.js │ │ ├── html5shiv.min.js │ │ ├── theme.js │ │ └── versions.js │ ├── language_data.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── sphinx_highlight.js │ ├── theme_overrides.css │ ├── underscore-1.13.1.js │ └── underscore.js ├── api │ ├── metrics.count_deletions.html │ ├── metrics.count_insertions.html │ ├── metrics.count_snvs.html │ ├── metrics.cross_contamination_rate.html │ ├── metrics.html │ ├── metrics.insert_size_std_deviation.html │ ├── metrics.mad_autosome_coverage.html │ ├── metrics.mean_autosome_coverage.html │ ├── metrics.mean_insert_size.html │ ├── metrics.pct_autosomes_15x.html │ ├── metrics.pct_reads_mapped.html │ ├── metrics.pct_reads_properly_paired.html │ ├── metrics.ratio_heterozygous_homzygous_indel.html │ ├── metrics.ratio_heterozygous_homzygous_snv.html │ ├── metrics.ratio_insertion_deletion.html │ ├── metrics.ratio_transitions_transversions.html │ └── metrics.yield_bp_q30.html ├── genindex.html ├── index.html ├── metrics.html ├── npm-sample-qc-overview.PNG ├── objects.inv ├── py-modindex.html ├── search.html └── searchindex.js ├── docsrc ├── Makefile ├── README.rst ├── _static │ └── theme_overrides.css ├── build.sh ├── conf.py ├── index.rst ├── make.bat └── metrics.rst ├── main.nf ├── modules ├── CollectMultipleMetrics │ └── main.nf ├── CollectVariantCallingMetrics │ └── main.nf ├── CollectWgsMetrics │ └── main.nf ├── bcftools │ └── main.nf ├── compile_aln_vcf │ └── main.nf ├── count_aln │ └── main.nf ├── count_variants │ └── main.nf ├── metric_aln │ └── main.nf ├── metric_variants │ └── main.nf ├── samtools │ └── main.nf └── verifybamid2 │ └── main.nf ├── nextflow.config ├── npm-sample-qc-overview.PNG ├── resources ├── README.rst ├── autosomes_non_gap_regions.bed ├── autosomes_non_gap_regions.interval_list └── verifybamid │ ├── 1000g.phase3.100k.b38.vcf.gz.dat.UD │ ├── 1000g.phase3.100k.b38.vcf.gz.dat.bed │ └── 1000g.phase3.100k.b38.vcf.gz.dat.mu ├── tests ├── NA06991_1000genomes-dragen-3.7.6 │ ├── output_certified │ │ └── results │ │ │ └── metrics │ │ │ └── NA06991.metrics.json │ ├── params.yaml │ └── run.sh ├── NA12878-chr14-AKT1_1000genomes-dragen-3.7.6 │ ├── NA12878-chr14-AKT1.bam │ ├── NA12878-chr14-AKT1.bam.bai │ ├── NA12878-chr14-AKT1.config │ ├── NA12878-chr14-AKT1.vcf.gz │ ├── NA12878-chr14-AKT1.vcf.gz.tbi │ ├── chr14_non_gap_regions.interval_list │ ├── output_certified │ │ └── results │ │ │ └── metrics │ │ │ └── NA12878-chr14-AKT1.metrics.json │ ├── params.aln.yaml │ ├── params.legacy.yml │ ├── params.vcf.yaml │ ├── params.yaml │ ├── readme.txt │ └── run.sh └── NA12878_1000genomes-dragen-3.7.6 │ ├── output_certified │ └── 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