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Best germline resource to use with latest gakt4 Mutect2?

bhaasbhaas Broad InstituteMember, Broadie

In the latest mutect2 tutorial

https://gatkforums.broadinstitute.org/gatk/discussion/24057/how-to-call-somatic-mutations-using-gatk4-mutect2#latest

there's mention of using af-only-gnomad.vcf file for the germline resource, but I didn't find a link to the resource to use.

If I google it, I find this:
http://bioinfo5pilm46.mit.edu/software/GATK/resources/
and
http://hgdownload.cse.ucsc.edu/gbdb/hg19/gnomAD/vcf/

If I go to the gatk wdl pipeline for the current mutect2 workflow:
https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl

it points to
https://gnomad.broadinstitute.org/downloads

Can you add a link to the exact resource file that should be used from the tutorial page?

Answers

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