gnomAD version in Mutect2 bundle
Hi, which version of gnomAD (2.x.x) and which cohort (exomes or genomes) was used to build the gnomAD VCF file (af-only-gnomad.raw.sites.b37.vcf) that you provide with your mutect2 resource bundle? Thanks.
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I don't think it is fair to push this to the community given that probably only the GATK team can really know the answer to this question... unless the scripts to generate the bundle at https://gatk.broadinstitute.org/hc/en-us/articles/360036212652-Resource-Bundle are made available somewhere... If you can at least link us to the team that maintains these bundles, that will be highly appreciated.
Thanks,
Pieter
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Pieter Lukasse Fair point. The script to generate the AF-only gnomAD is public and available in the gatk repo: https://github.com/broadinstitute/gatk/blob/master/scripts/mutect2_wdl/mutect_resources.wdl.
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Thanks David Benjamin! I will check it out.
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