How can I make a BED file from a VCF file?

Question

[VictoriaP]

I have ~60 .vcf files with multiple viral insertion data. I need to create a bed file from these to use with bedtools.

How do I create a BED file from a VCF file/multiple VCF files?

[Ram]

BED and VCF are formats. Information content wise, VCF has more information than basic 3-field BED, so extracting a BED out of a VCF should be pretty straightforward.

The question here is - are you looking to extract one BED per VCF, or are you looking to combine the information content from the VCF and get a BED that represents some sort of operation on this information content? Perhaps a BED file with all variants found across any of the 60 VCF files or a BED file with variants found in all of the 60+ VCF files?

[VictoriaP]

Thanks, I finally managed it. I needed to make a single BED file with all of the HERV viral insertion points identified from all of the 60+ files.

... Now to figure out how to properly use bedtools closest.

Answer 1

[Brice Sarver]

Check out vcf2bed in BEDOPS. You can also try searching this site for more advice.

[VictoriaP]

Thank you! This site was really helpful!

[Ram]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work.