1000 Genomes GVF Format

[NextGenSeq]

Does anyone know the link to download 1000 Genomes human SNPs in GVF format?

I can only find VCF format and am clueless on converting it to GVF.

[laura]

The 1000 Genomes project does not distrubute any data in GVF format

You can get the pilot snps on GRCh37 in GVF format from Ensembl

ftp://ftp.ensembl.org/pub/release-62.../homo_sapiens/

For how to convert between the 2 formats I would suggest writing something your self using the description here

http://www.sequenceontology.org/resources/gvf.html

as I don't think anyone else has written a converter yet

[NGSfan]

GVF to VCF converter

I have written a GVF to VCF converter (only in that direction)

It is available on google code now.

http://code.google.com/p/gvf2vcf/

if someone likes, they can make a VCF to GVF converter... I'm not yet planning to make one (unless the need arises)

Disclaimer: use at your own risk!! please report bugs/ideas

[yingchen]

Sorry for bumping this 4 years old thread. I tried to get the code for gvf2vcf.pl, but the link is broken. Is there another link to get the code?

Thanks,

Ying

[dan]

Here is a different script to do the same:

https://github.com/Ensembl/ensembl-variation/blob/master/scripts/misc/gvf2vcf.pl