I am trying to merge two imputed (I used SHAPEIT and IMPUTE2) binary file sets with PLINK's
bmerge command, but this error pops up:
Error: Identical A1 and A2 alleles on line 1
I am pretty sure I've got many single-allele SNPs in my data, so I was wondering if there is a quick way to solve this problem? I checked PLINK's manual, but there seems to be no way to ignore such SNPs or correct them.
I would like to avoid - if possible - to look for a solution in SHAPEIT or IMPUTE2, because prephasing and imputation already took a very long time to run.