Question: Snpsift to filter a number of genes
0
gravatar for krithika.gu
4.2 years ago by
krithika.gu260
United States
krithika.gu260 wrote:

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

ADD COMMENTlink written 4.2 years ago by krithika.gu260

old questioun, but I need exactly the same and get it to work using ANN[*].GENE

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Jimbou730
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