Question: Merging inconsistencies in PLINK
gravatar for GabrielMontenegro
19 months ago by
United Kingdom
GabrielMontenegro520 wrote:

I am trying to merge two different PLINK files genotyped on the same platform. However, I found some inconsistencies that could not be solved by the --flip command. I checked the SNPs that could not be merged after the flip and found this type of problem:

File 1:

4    rs10000432    68.93    47511781    T    C

File 2:

4    rs10000432    68.93    47511781    A    C

One of the alleles is different, while the other allele is the same on both files.

What should I do on this case? I wasn't expecting to find these type of issues on these datasets since both were genotyped on the same platform.

snp plink • 939 views
ADD COMMENTlink modified 17 months ago by Biostar ♦♦ 20 • written 19 months ago by GabrielMontenegro520

Just an initial comment: for that particular SNP, the ancestral 'reference' allele is C (

When you attempted to merge the first time, PLINK may have output a file with the extension *.missnp, which would contain these multi-allelic sites. You can remove these from your dataset with the following command:

plink --noweb --bfile MyData1 --exclude MyData.missnp --make-bed --out MyData1.Pruned ;
plink --noweb --bfile MyData2 --exclude MyData.missnp --make-bed --out MyData2.Pruned ;

Then attempt to merge again.

If you don't want to necessarily remove these, then you may have to do more rigorous data preparation. In which format was your data initially - VCF?? It would be useful to run every genotype against a reference genome and ensure that the ref>alt order is maintained.

ADD REPLYlink modified 19 months ago • written 19 months ago by Kevin Blighe41k
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