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  • converting vcf between different assemblies

    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

  • #2
    There's a LiftOverVCF.pl tool from the Broad that uses GATK to liftover a VCF from one build to another.

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