Snpsift to filter a number of genes
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5.3 years ago
kay ▴ 290

Hello,

I have a VCF file, and would like to pull out all variants in various genes of interest (I have about 200 genes)

I created a txt file with all my genes of interest.

cat variants.vcf | java -jar SnpSift.jar filter --set input.txt "EFF[*].GENE in SET[0]" > filtered.vcf

This seemed to filter out all the variants, and I got an empty VCF File without any variants.

  • Is the SET function not meant to be used like this ?
  • Do I have to use a loop instead ?

Could someone help with this ?

Thanks, K

SNP variant annotation snpsift snpeff • 1.9k views
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old questioun, but I need exactly the same and get it to work using ANN[*].GENE

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