Question: Snpsift to filter a number of genes
0
gravatar for krithika.gu
5.0 years ago by
krithika.gu280
United States
krithika.gu280 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 5.0 years ago by krithika.gu280

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

ADD REPLYlink modified 11 months ago • written 11 months ago by Jimbou820
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1831 users visited in the last hour
_