somatic wgs does not include gnomad filtering

wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL

MIT License

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somatic wgs does not include gnomad filtering #48

Open chrisamiller opened 2 years ago

chrisamiller commented 2 years ago

we use it in exome, in the filter_vcf step, but the gnomad vcf we're using is only a subset, restricted to exome coords. Would be nice to revisit that decision at some point (options: leave it out, apply it to exome only, or find a new genome-wide VCF)

malachig commented 1 year ago

presumably we can now get a genome-wide VCF from GNOMAD v3 which would seem a good solution here.