removing indels in plink

Question

I have data in Plink format. I removed Indels using --snps-only command in Plink, but still some snps are as below:

rs58119544;rs5746975    0   16915280    T   A

I wonder, how i can get rid of these snps? the correct should be single snps without this (;) sign. Any idea to fix it please?

Answer 1

Use grep to get SNPs that have ";" in the name:

>$ grep ";" myMap.txt | cut -f1 -d" " > myBadSNPs.txt

Then use plink with --exclude :

plink --file myFile
--exclude myBadSNPs.txt
--out myFileFiltered