convert vcf into bed format

nans_bn

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Join Date: Mar 2011

Posts: 12
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convert vcf into bed format

08-01-2011, 11:34 PM

Hi,

I have set of (huge) data mapped against hg19 build and generated SNPs in gff3 and vcf format. Now I would like to use lift over hg19->hg18 .
I would like to know if LiftOver supports gff3 and vcf format,

liftOver -gff3 oldFile hg19ToHg18.over.chain newFile unMapped

if not, is there any method in which we can convert these formats into BED format ?

Thank you...

Last edited by nans_bn; 08-02-2011, 04:22 AM.
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