How to filter out the SNPs with deletion allel ?


I'm wondering whether there are a way to filter out the SNPs with deletion allel (*). I'm just not confident enough to keep these snps so I prefer rather discard them rather than having false snp.
However, in VariantFiltration or SelectVariants, there seems to be no option to filter or discart this type of SNPs.

I'm looking forward to having your response.


Best Answer


  • nkobmoonkobmoo ParisMember

    Actually, it's what I did. I use AWK to look for rows containing * and just remove it. I think it is the easiest way. Still, if in the future, you could include this option in the pipeline, it would be a good idea.

  • shleeshlee CambridgeMember, Broadie, Moderator

    I've put in such a feature request here on your behalf. If such features become a part of SelectVariants, then you'll see them in GATK4 tools.

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