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filter intergenic region structural variants #71

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prasundutta87 opened this issue May 31, 2022 · 0 comments
Open

filter intergenic region structural variants #71

prasundutta87 opened this issue May 31, 2022 · 0 comments

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@prasundutta87
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prasundutta87 commented May 31, 2022 •
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Hi,

I am using this command to remove intergenic_region variants. However, intergenic variants still remain in the resulting VCF. Can I please be helped with this? Before using SnpSift, I annotated my structural variation VCF (produced using sniffles2) using snpEff v5.1.

SnpSift filter "!(ANN[*].EFFECT has 'intergenic_region')" <input>.vcf > <output.vcf>
SnpSift version 4.3t (build 2017-11-24 10:18)

Regards,
Prasun
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