I am trying to merge two .ped (GA_142_merged-omni-ga and removed.ped) files with below commands but getting error.
This is command I am using:
plink --file GA_142_merged-omni-ga --merge removed.ped removed.map --recode --out merged
Variant 'rs2040369' is not biallelic. To obtain a full list of merge failures, convert your data to binary format and retry the merge.
Any one having such issue earlier too !!