Question about the resolution of alleles reported in ./resources/1000G.bglv4.bgl.phased.vcf.gz

immunogenomics / HLA-TAPAS

HLA-TAPAS pipeline for HLA association and fine-mapping studies

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Question about the resolution of alleles reported in ./resources/1000G.bglv4.bgl.phased.vcf.gz #7

Closed brettva closed 3 years ago

brettva commented 3 years ago

@WansonChoi

Is it correct that all alleles reported in the ID col of ./resources/1000G.bglv4.bgl.phased.vcf.gz we actually translated from g-group resolution data? If so did this translation occur by using the NomenCleaner module? (ie just the first compatible 4 field allele was reported when one g-group mapped to multiple 4 field alleles?

Just checking my understanding, thank you!

WansonChoi commented 3 years ago

@brettva

Given output of HLA-TAPAS, It's correct. all HLA alleles reported in the ID column will be G-group resolution because essentially HLA type input of HLA-TAPAS is G-group resolution data. Though HLA alleles may look 4-field nomenclature due to NomenCleaner, they are G-group resolution alleles in origin.