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Converting A Snp Gff3 File To Vcf Format

Hi there,

I've got a GFF3 file containing SNP's and would like to convert it to VCF. GATK doesn't seem to recognise GFF SNP files and a quick google search and look in SEQanswers doesn't reveal any tools to do it. Else, I'll have to write a perl script myself, but it would be good to use something else if its out there.

Thanks, Chris

snp gff vcf
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updated by Brugger • Brugger • written by Chris Penkett • Chris Penkett

can you post a sample of your GFF3 file please ?

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written by Pierre Lindenbaum Pierre Lindenbaum

2 answers

It looks like there is a script to do convert GFF4 to VCF at http://www.pacbiodevnet.com/ConversionTools . It may support GFF3 as well, but if not it may be faster to modify this than create one from scratch.

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written by Mrawlins • Mrawlins

Nice pointer. I signed up for a PacBio dev account to look at the scripts. It turns out that this is a GFF3 to VCF confusion tool; as far as I know there isn't a GFF4 format yet so that's a typo on the description page. The scripts do require GFF3 in a certain format, as would any program that did this conversion since there is more than one way to represent variations in GFF.

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written by Brad Chapman Brad Chapman

I get an error. pkg_resources.DistributionNotFound: pbpy==0.1

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written by Raymond301 • Raymond301

Here is the v4.0 specifications.

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updated by Ram Ram • written by Brugger • Brugger

The 1000genomes website back end has changed; this is the url now is now.

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updated by Ram Ram • written by Laura Laura

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