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Different resource for Mutect2/GetPileupSummaries when dealing with genome data


Firstly, could someone please set the category for this question to the most relevant? For some reason it's only letting me select Zoo & Garden from the menu.

I'm currently using GATK, following the best practices for somatic variant calling. I already have this set up for exomes, but I'm now attempting to run the same pipeline on genome data.

I'm using the gnomAD "af-only-gnomad.raw.sites.b37.vcf" file as the germline resource for Mutect2, and I'm using the "small_exac_common_3_b37.vcf.gz" file (both from the bundle) as the -V and -L arguments for GetPileupSummaries when running exomes - are these the correct resources for genomes as well? Or is there another resource you recommend?


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