🐍 hydra-genetics/mitochondrial

Snakemake module for performing Mitochondrial short variant discovery

💬 Introduction

The module consists of rules to call mitochondrial variants from .bam files. Mitochondorial SNV and Indels are called using mutect2 following the GATK Best Practice Workflow for mitochondrial short variants.

❗ Dependencies

In order to use this module, the following dependencies are required:

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🎒 Preparations

Sample data

Input data should be added to samples.tsv and units.tsv. The following information need to be added to these files:

Column Id	Description
samples.tsv
sample	unique sample/patient id, one per row
units.tsv
sample	same sample/patient id as in samples.tsv
type	data type identifier (one letter), can be one of Tumor, Normal, RNA
platform	type of sequencing platform, e.g. NovaSeq
machine	specific machine id, e.g. NovaSeq instruments have @Axxxxx
flowcell	identifer of flowcell used
lane	flowcell lane number
barcode	sequence library barcode/index, connect forward and reverse indices by +, e.g. ATGC+ATGC
fastq1/2	absolute path to forward and reverse reads
adapter	adapter sequences to be trimmed, separated by comma

✅ Testing

The workflow repository contains a small test dataset .tests/integration which can be run like so:

$ cd .tests/integration
$ snakemake -s ../../Snakefile -j1 --use-singularity

🚀 Usage

To use this module in your workflow, follow the description in the snakemake docs. Add the module to your Snakefile like so:

module mitochondrial:
    snakefile:
        github(
            "hydra-genetics/mitochondrial",
            path="workflow/Snakefile",
            tag="1.0.0",
        )
    config:
        config


use rule * from mitochondrial as mitochondrial_*

Output files

The following output files should be targeted via another rule:

File	Description
mitochondrial/gatk_select_variants_final/{sample}_{type}.vcf	mitochondrial .vcf from mutect2
mitochondrial/gatk_collect_wgs_metrics/{sample}_{type}_mt.metrics.txt	mitochondrial coverage metrics .txt from CollectWgsMetrics

🧑‍⚖️ Rule Graph