Snakemake workflow for implementing GATK best practices SNP and INDEL variant calling on the mitochondrial genome (Laricchia et al 2021. BioRxiv).

Final output files that are retained by the overall workflow include:

• {SAMPLE_IDS}_mtdnacn.txt: autosome and mitochondrial coverage and estimated mtDNAcn
• {SAMPLE_IDS}_chrM.bam: Subseted mitochondrial bam file from original input files
• {SAMPLE_IDS}_chrM_per_base_coverage.tsv: Proivdes coverage at each base - used for generating joint vcf file.
• {SAMPLE_IDS}_chrM_contamination.raw.txt: Output of haplochecker providing estimated contamination levels and mitochondrial haplogroups
• {SAMPLE_IDS}_chrM_metrics.txt: Coverage meterics of mitochondrial genome from CollectWgsMetrics.
• {SAMPLE_IDS}_chrM_theoretical_sensitivity.txt: Theoretical Sensitivity of mitochondrial genome from CollectWgsMetrics.
• {SAMPLE_IDS}_chrM.duplicate_metrics: Output from MarkDuplicates.

Intermediate files can be retained by using --notemp