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Handle new gnomAD fields in variants sets (when launched from Mosaic) #878

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tonydisera opened this issue Nov 23, 2022 · 2 comments
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@tonydisera
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There are following new gnomAD v2 fields:
If we want to use v2.1.1 genomes, we need the following:
gnomad_allele_count__v2_1_1_genomes__c640bcce
gnomad_allele_frequency__v2_1_1_genomes__774720c3
gnomad_allele_number__v2_1_1_genomes__e944a1c3
gnomad_depth__v2_1_1_genomes__b98619e8
gnomad_homozygotes__v2_1_1_genomes__96b1d837
gnomad_popmax_af__v2_1_1_genomes__c14fd0d2

@AlistairNWard, do we have gnomad v3 fields for variants from a GRCh38 build?

@tonydisera tonydisera added this to the gene_4.6.12 milestone Nov 23, 2022
@tonydisera tonydisera self-assigned this Nov 23, 2022
@AlistairNWard
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We do:
gnomad_allele_count__v3_1_2_genomes__84b78114
gnomad_allele_frequency__v3_1_2_genomes__bfceffd3
gnomad_allele_number__v3_1_2_genomes__fab93285
gnomad_homozygotes__v3_1_2_genomes__902eb14e
gnomad_popmax_af__v3_1_2_genomes__3e5ec14b
gnomad_variant_depth__v3_1_2_genomes__75d9ee5c

We also have v2 exomes:
gnomad_allele_count__v2_1_1_exomes__91cea8bf
gnomad_allele_frequency__v2_1_1_exomes__32186614
gnomad_allele_number__v2_1_1_exomes__0f20a21f
gnomad_depth__v2_1_1_exomes__756197fd
gnomad_homozygotes__v2_1_1_exomes__60ad3630
gnomad_popmax_af__v2_1_1_exomes__4c2af7e5

@AlistairNWard
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All the above are for GRCh38. Also of note - an empty value doesn't mean that there is no value in gnomAD, only that there is no annotation in Mosaic

@tonydisera tonydisera modified the milestones: gene_4.6.12, gene_4.7 Jan 13, 2023
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