How to extract regions from abed file based on variants in vcf file

Question

[Kash]

Hi everyone,

I have a vcf file and a bed file which contains region information for some of the variants in vcf file. I want to extract the regions in the bed file which are corresponding to the variants in the vcf file. Can someone please tell me how I can do this? I know vcf tools can filter a vcf file using a bed file, but here I want to filter the bed file based on vcf file and out put the regions in bed file.

Answer 1

[Alex Reynolds]

One way, via bedops and vcf2bed:

$ bedops -e 1 <(sort-bed regions.bed) <(vcf2bed < variants.vcf) > answer.bed

If you want the associations between regions and SNPs, you could use bedmap:

$ bedmap --echo --echo-map --skip-unmapped --delim '\t' <(sort-bed regions.bed) <(vcf2bed < variants.vcf) > answer.bed

This prints each region and those variants which overlap a region. If a region does not contain any variants, --skip-unmapped skips over that region.

Reference:

• https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html#element-of-e-element-of
• https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/vcf2bed.html
• https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html#echo