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

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?

bed bedtools
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updated by Ram Ram • written by VictoriaP • VictoriaP

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?

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written by Ram Ram

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.

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written by VictoriaP • VictoriaP

1 answer

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

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written by Brice Sarver Brice Sarver

Thank you! This site was really helpful!

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written by VictoriaP • VictoriaP

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.

Upvote|Bookmark|Accept

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written by Ram Ram

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