Utilize gnomAD v4.1 joint exome+genome allele counts and frequencies.

[tonydisera]

• Refresh backend to use gnomAD 4.1 (joint genomes+exomes). Create stripped down version of gnomAD 4.1 vcf to the minimal set of INFO fields. The minimal set will have 3 sets, for exomes, genomes, and merged. @anderspitman

• Provide the minimal set of INFO fields (3 subsets for exomes, genomes, merged). @tonydisera

• Change parsing code (vcf.iobio.js) to pull from merged allele frequency. This will result in default filtering on merged allele frequencies instead of genomes only. @tonydisera

• Change VariantInspectCard and popup (stratified by ethnicity group). @tonydisera

• Review export code. @tonydisera

[anderspitman]

@tonydisera currently we only have 2 files per gnomad version, exomes and genomes, is that correct? Is merged something new?

[tonydisera]

Hi @anderspitman - I'm talking about join-called gnomAD 4.1 vcf I mentioned on Slack a few days ago:

If possible, it would be great to use thejoint-called gnomAD 4.1 vcf. This has both genomes and exome as well as combined allele frequencies.
The downside is these are bigger files than the genomes only. For example, chr22 is genomes only = 14GB vs joint = 21GB
https://gnomad.broadinstitute.org/downloads

[anderspitman]

@tonydisera sorry I think I completely missed that Slack message originally. I'll be sure to use the joint files for our 4.1 upgrade.