The numbers of SNPs are not consistent

[JingjingBai2021]

Hi , I am using Hibag for HLA imputation. My dataset is GSA genotyped data.

I found when I use the function "hlaBED2Geno" to import the genotype data, there are around 8000 SNPS in the MHC region. But when I use plink to extract MHC region from my genotype data, there are around 40,000 SNPs.

I am wondering where the discrepancy comes from. And for the HLA Manhattan plot, I am trying to merge the SNPs in the MHC region with imputed HLA alleles. Is there any function that I can use in HIBAG to accomplish that?

Thank you in advance!

[zhengxwen]

     hlaBED2Geno(bed.fn, fam.fn, bim.fn, rm.invalid.allele=FALSE,
         import.chr="xMHC", assembly="auto", verbose=TRUE)

Set import.chr="6", try it again.