Removing SNPs with the count allele in 5 (insertion), 6 (deletion) or 7(allele from a reference panel)
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20 months ago
jongyun.jung ▴ 10

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.

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

Thank you.

plink SNP imputation unix gwas • 453 views
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20 months ago
 awk '($4 ~/^[ATGC]$/ && $5 ~/^[ATGC]$/)'
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Thank you for your help!

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