Currently working on a project to do mitochondrial variant calling on whole exome data. Our probes are about 120 bp and are setup to capture the entirety of the chrM contig at extremely high depth.
We're currently looking at a few different tools, and the new GATK best practices MUTECT2 mito pipeline that incorporates a double alignment strategy looks very promising. The thing is, the --mitochondria-mode tag is brand spanking new, and there just isn't a lot of documentation or usage examples for replicating the pipeline at the command line. I've tried contacting support a few times, but GATK support is quite understaffed at the moment.
Thinking instead that we might use their fully built TERRA cloud pipeline (found here) to generate our vcfs, but the pipeline docs indicate that the workflow is configured for full WGS bam/crams, not WES bam/crams.
People who are familiar with TERRA and variant calling... do you think it is possible to do WES on this workflow? What required inputs would need to change? I'm guessing a few of the interval lists?
Also, there are quite a few optional inputs you can use. Can anyone suggest some I might want to use besides setting a vaf_filter_threshold?