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" > 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 ?