Question: Removing SNPs with the count allele in 5 (insertion), 6 (deletion) or 7(allele from a reference panel)
0
gravatar for jongyun.jung
11 months ago by
jongyun.jung10
USA
jongyun.jung10 wrote:

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.

unix snp plink imputation gwas • 281 views
ADD COMMENTlink modified 11 months ago by Pierre Lindenbaum129k • written 11 months ago by jongyun.jung10
1
gravatar for Pierre Lindenbaum
11 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:
 awk '($4 ~/^[ATGC]$/ && $5 ~/^[ATGC]$/)'
ADD COMMENTlink written 11 months ago by Pierre Lindenbaum129k

Thank you for your help!

ADD REPLYlink written 11 months ago by jongyun.jung10
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