├── .editorconfig ├── .gitattributes ├── .github └── workflows │ └── main.yml ├── .gitignore ├── .gitmodules ├── .snakemake-workflow-catalog.yml ├── .test ├── config │ ├── config.yaml │ ├── samples.tsv │ └── units.tsv ├── data │ ├── known_variants.vcf │ ├── reads.1.fq.gz │ └── reads.2.fq.gz └── report.html ├── LICENSE ├── README.md ├── config ├── README.md ├── config.yaml ├── samples.tsv └── units.tsv └── workflow ├── Snakefile ├── envs ├── bedops.yaml ├── rbt.yaml ├── samtools.yaml └── stats.yaml ├── report ├── calls.rst ├── depths.rst ├── freqs.rst ├── multiqc.rst ├── stats.rst ├── vcf.rst └── workflow.rst ├── rules ├── annotation.smk ├── calling.smk ├── common.smk ├── filtering.smk ├── mapping.smk ├── qc.smk ├── ref.smk └── stats.smk ├── schemas ├── config.schema.yaml ├── samples.schema.yaml └── units.schema.yaml └── scripts ├── common.py └── plot-depths.py /.editorconfig: -------------------------------------------------------------------------------- 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