how to extract the variants using Bed file

Question

[k.manojkumar2991]

Hello all,

Sorry if this has been answered before (though I have not found an appropriate answer already) What is an effective way to extract multiple variants from the vcf file using bed file.

I have a huge number of variants in vcf. example i have downloaded the human whole genome vcf. but i am looking for certain exons variants and i have those position in the bed file. i want to find only check those positions alone not the whole vcf. how to extract the variants using Bed file 

Answer 1

[christopher medway]

The site filtering options in VCFtools has a --bed command, which allows the user to extract or filter variant using a bed file. 

[christopher medway]

http://vcftools.sourceforge.net/man_latest.html