converting vcf between different assemblies

[krawitz]

Hi,

let's suppose you have got a variant data set in vcf format. It indicates in the header that genomic coordinates refer to a certain assembly (##reference=hg19). Now you want to convert it to another built, let's say hg18.

A laborious and buggy solution would be the following: convert vcf to bed or gff, use the liftOver tool from ucsc convert back to vcf.

Does anyone know a better solution?

Thanks!

Peter

[vasisht]

There's a LiftOverVCF.pl tool from the Broad that uses GATK to liftover a VCF from one build to another.

http://www.broadinstitute.org/gsa/wiki/index.php/LiftOverVCF.pl