Removing SNPs with the count allele in 5 (insertion), 6 (deletion) or 7(allele from a reference panel)

Question

[jystat]

Hi,

I have imputed data and renamed the integers allele to the letters by using the plink falg of "allele 1234".

However, I have noticed that there are 5 (insertion), 6 (deletion) or 7(allele from a reference panel) not changing to the letters.

Can anyone know how to delete this SNPs in plink or any other software?

Thank you.

Answer 1

[Pierre Lindenbaum]

 awk '($4 ~/^[ATGC]$/ && $5 ~/^[ATGC]$/)'

[jystat]

Thank you for your help!