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
Please sign in to leave a comment.