Mitochondrial pipeline requirement
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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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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Hello,
According to the MT pipeline, this step is calculated after subsetting to chrM. Only chrM is present in the BAM file. How can the autosomal coverage be calculated? There seems to be an issue in this part of the pipeline. Should I get the mean coverage information from the full BAM file instead?
Thanks -
Hi Sinem Selvi
You need to calculate autosomal coverage using the full whole genome bam file Using CollectWgsMetrics tool (not to confuse yourself with the one mentioned in the pipeline. That one is for MT coverage only) and provide that as an input. This parameter was used by earlier versions of FilterMutectCalls tool for the parameter named
--autosomal-coverage
which is no longer available in the newest releases. Make sure that you use a version that has this parameter if you are planning to use autosomal coverage filter activated by FilterMutectCalls.
If you are using a later version this parameter is used within new tools added to the workflow named NuMTFilterTool.
Regards.
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Thank you! NuMTFilterTool looks better to use.
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