The numbers of SNPs are not consistent

Question

The numbers of SNPs are not consistent

Opened this issue a year ago · 1 comments

JingjingBai2021 commented a year ago

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!

Answer 1 · 2023-05-11T19:46:55.000Z

     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.