How do I filter my VCF file to only include certain coordinates from a BED file?

Question

[joomi]

Hello,

I have a VCF file and a BED file in the form of <chr> <start> <end>. How do I filter my VCF file to include SNPs that are within the coordinates of the BED file?

Thank you!!

Answer 1

[cmdcolin]

BEDTools has the ability to process VCF (and BED too of course), so you can use "bedtools intersect" with the VCF and BED file as input

Hope that helps

[joomi]

Thank you very much!!

[finswimmer]

Hello and welcome jommi,

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 if they work.

fin swimmer