Scripts for facilitating execution of HIBAG to infer classical HLA genotypes for subjects based on SNV genotypes using public domain reference datasets
In v2.0.0, advise not to use output of whole-genome imputation's alignment step as this removes variants not in the 1000 Genomes reference haplotypes. Don't specify what QC should be done (e.g. remove monomorphic? test HWE? what threshold, which pops?)
In v2.0.0, advise not to use output of whole-genome imputation's alignment step as this removes variants not in the 1000 Genomes reference haplotypes. Don't specify what QC should be done (e.g. remove monomorphic? test HWE? what threshold, which pops?)