Question: Changing Genome Coordinates For Vcf
3
gravatar for Jts
8.0 years ago by
Jts1.2k
Jts1.2k wrote:

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.

vcf • 4.8k views
ADD COMMENTlink modified 5.1 years ago by Biostar ♦♦ 20 • written 8.0 years ago by Jts1.2k
3
gravatar for Adam
8.0 years ago by
Adam990
United States
Adam990 wrote:

GATK provides a tool for this:

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

ADD COMMENTlink written 8.0 years ago by Adam990
0
gravatar for Jorge Amigo
8.0 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Jorge Amigo11k

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.

ADD REPLYlink written 8.0 years ago by Jts1.2k

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

ADD REPLYlink written 8.0 years ago by Jorge Amigo11k
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