Problem while merging two .ped files.

Question

[always_learning]

Hey All,

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

Error:

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 !!

Thanks
Syed

Answer 1

[russhh]

Does adding

--missing-genotype N

or similar fix this?

Answer 2

[Maxime Lamontagne]

Transform both of your files in binary format (bed/bim/fam --make-bed) and look in the bim file the two last columns. If the alleles are not the same in the two files you found your error. Maybe some SNPs are not on the same strand.