Only 4 SNPs are left, in line 128 of DISH.r 😮

[jielab]

Hi, there:

I tested your DISH.r script.

After I run line 128, temp_pos <- temp[(temp$Major==temp$Effect_allele & ... , I found that only 4 SNPs are left.

The original Ref_map file has 8961 records, and the original study_map file has 1542 records. Only 4 typed SNPs could impute HLA?

Also, since your reference panel is construcuted several years ago, can you please let me know how to use the latest HLA imputation reference panel?

Thank you & best regadrs,
Jie