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.
2 answers
GATK provides a tool for this:
http://www.broadinstitute.org/gsa/wiki/index.php/LiftOverVCF.pl
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.
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
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