Converting A Snp Gff3 File To Vcf Format

Question

[Chris Penkett]

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

[Pierre Lindenbaum]

can you post a sample of your GFF3 file please ?

Answer 1

[Mrawlins]

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.

[Brad Chapman]

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.

[Raymond301]

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

Answer 2

[Brugger]

Here is the v4.0 specifications.

[Laura]

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