How to subset the mutations that occur just in my interest genes within the vcf file?

Question

[Zahra]

Hi all,

I have a vcf file that I perform the BED file by vcftools to subset the mutations in my interest genes. I have downloaded the BED file from the UCSC (selecting the BED file for the whole gene of my gene list). However, after performing the vcftools, I have found some mutations in genes that weren't in my gene list. How to subset the mutations that occur just in my interest genes?

Thanks for any help.

Answer 1

[ATpoint]

Extract Sub-Set Of Regions From Vcf File

Use tabix, http://www.htslib.org/doc/tabix.html, and see its -R option to only retrieve VCF entries that overlap the BED file you provide for that argument. That would need to be a BED file with the coordinates you are interested in, e.g. the entire gene interval, or its exons. You could get the coordinates directly from a reference GTF file.