Question: Problem while merging two .ped files.
2
gravatar for always_learning
5.6 years ago by
always_learning1.0k
Doha, Qatar
always_learning1.0k wrote:

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

ped plink bed • 2.8k views
ADD COMMENTlink modified 5.6 years ago by Maxime Lamontagne2.2k • written 5.6 years ago by always_learning1.0k
1
gravatar for russhh
5.6 years ago by
russhh5.1k
UK, U. Glasgow
russhh5.1k wrote:

Does adding

--missing-genotype N

or similar fix this?

ADD COMMENTlink written 5.6 years ago by russhh5.1k
0
gravatar for Maxime Lamontagne
5.6 years ago by
Québec
Maxime Lamontagne2.2k wrote:

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.

ADD COMMENTlink written 5.6 years ago by Maxime Lamontagne2.2k
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