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

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.

1

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

Thank you.

plink snp imputation unix gwas
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by jystat • jystat

1 answer 

 awk '($4 ~/^[ATGC]$/ && $5 ~/^[ATGC]$/)'
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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you for your help!

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written by jystat • jystat

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