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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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How to filter out the SNPs with deletion allel ?
nkobmoo
ParisMember ✭
Hi,
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.
Cheers
Best Answer
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shlee
Cambridge ✭✭✭✭✭
Hi @nkobmoo,
SelectVariants can subset out indels but not insertions or deletions in isolation. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Please refer to the documentation here.
I think your other option is to use AWK to filter based on column contents. I have to think about this more.
I'll follow up on this thread if I think of anything.
Answers
Hi @nkobmoo,
SelectVariants can subset out indels but not insertions or deletions in isolation. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Please refer to the documentation here.
I think your other option is to use AWK to filter based on column contents. I have to think about this more.
I'll follow up on this thread if I think of anything.
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.
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.
Hi shlee,
I came across this post but couldn't find in the documentation what do type MIXED, MNP, SYMBOLIC, NO_VARIATION mean?
Thanks,
Wen
Hi @wenluo,
Article#3682 describes the variant types.