Changing Genome Coordinates For Vcf

Question

[Jts]

I have a VCF file which uses hg18/NCBI36 coordinates. I would like to convert the coordinates to GRCh37 to compare the variants with a more recent data set. Is there a tool to perform this conversion? One way to do it would be to convert the variants to BED then use UCSC liftOver. Before writing this myself, I thought I should check if someone else has solved this problem first.

Answer 1

[Adam]

GATK provides a tool for this:

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

Answer 2

[Jorge Amigo]

you will find several posts on this matter if you just search BioStar for "hg18 hg19" for instance.

UCSC liftOver and Ensembl Assembly Converter are the most suggested options.

[Jts]

Hi Jorge, thanks for the pointer but I am specifically looking for a tool to convert a VCF file. I believe that liftover/ensembl require BED or GFF input. It is not a difficult conversion but it would be nice if a standard tool existed to do this.

[Jorge Amigo]

oh, I see. unfortunately I don't know of such tool that would translate coordinates from a VCF file directly, so I guess you'll have to extract them yourself and then upgrade them using any of the mentioned tools. for the coordinates extraction theres a post on seqanswers describing some awk and sed scripting that may be helpful: http://seqanswers.com/forums/showthread.php?t=9132