Mitochondrial pipeline requirement

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Sheryl

• June 15, 2023 01:55

I am wanting to use the GATK best practice for mitochondrial SNVs and indel variants.

I read from here https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-  "Expected Input:
This workflow requires a WGS h38 CRAM or BAM file and the median of the coverage over the autosome" 

How do I calculate the "median of the coverage over the autosome" please?

I'm very confused about it's use. At the Mutect2 part it states: "--median-autosomal-coverage argument (default 0) activates a recommended filter against likely erroneously mapped NuMTs (nuclear mitochondrial DNA segments). For the value, provide the median coverage expected in autosomal regions with coverage."

So do we set this to 0 or not 0? (and if not 0 how do I calculate this figure please?)

I also couldn't see this anywhere in the input.json for the wdl from here: https://github.com/gatk-workflows/gatk4-mitochondria-pipeline/tree/master 

 

 

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  SkyWarrior

  • June 26, 2023 09:33

  Hi Sheryl

  I guess the pipeline requires you to calculate median coverage over autosomes using CollectWGSMetrics workflow or any other equivalent tool before you start working on variant calling over MT. 

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