gnomAD version in Mutect2 bundle

March 03, 2020 20:28

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.

4 comments

Bhanu Gandham

March 04, 2020 00:03
Hi ,

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Pieter Lukasse

March 04, 2020 21:54

Edited
Hi Bhanu Gandham,

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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David Benjamin

March 05, 2020 18:01
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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Pieter Lukasse

March 06, 2020 16:52
Thanks David Benjamin! I will check it out.
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