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

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!!

rna-seq snp

1 answer

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

Thank you very much!!

Hello and welcome jommi,

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fin swimmer

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