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Questions about Mutect2, about --germline-resource source

I am doing clinical analysis, and in most of the case my data belongs to one individual. So I don't have a batch of Normal samples to create PoN. I wonder what effect/bias will happen if missing this step.

Also I am trying to use the parameter "--germline-resource", but I found the af-only-gnomad.raw.sites.b37.vcf.gz file (while I use hg19; downloaded from ftp://ftp.broadinstitute.org/bundle/Mutect2/) includes sites only belong to chromosome 1. I wounder if this is a complete version, or I should downloaded this dataset by myself? (http://gnomad.broadinstitute.org/downloads)

Thank you.

Answers

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