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Old 05-24-2011, 08:21 AM   #1
NextGenSeq
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Default 1000 Genomes GVF Format

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.
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Old 06-16-2011, 05:48 AM   #2
laura
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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
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Old 08-18-2011, 04:29 AM   #3
NGSfan
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Default 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
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Old 06-25-2015, 05:50 AM   #4
yingchen
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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
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Old 07-19-2016, 12:50 AM   #5
dan
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Here is a different script to do the same:
https://github.com/Ensembl/ensembl-v...isc/gvf2vcf.pl
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