Question: Converting A Snp Gff3 File To Vcf Format
6
gravatar for Chris Penkett
9.3 years ago by
Chris Penkett480
Cambridge, UK
Chris Penkett480 wrote:

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

vcf gff snp • 5.4k views
ADD COMMENTlink written 9.3 years ago by Chris Penkett480
1

can you post a sample of your GFF3 file please ?

ADD REPLYlink written 9.3 years ago by Pierre Lindenbaum124k
4
gravatar for Mrawlins
9.2 years ago by
Mrawlins420
Retirement
Mrawlins420 wrote:

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.

ADD COMMENTlink written 9.2 years ago by Mrawlins420

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.

ADD REPLYlink written 9.2 years ago by Brad Chapman9.5k

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

ADD REPLYlink written 7.7 years ago by Raymond301140
0
gravatar for Brugger
9.2 years ago by
Brugger0
Brugger0 wrote:

Here is the v4.0 specifications.

ADD COMMENTlink modified 3 months ago by RamRS25k • written 9.2 years ago by Brugger0
1

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

ADD REPLYlink modified 3 months ago by RamRS25k • written 9.0 years ago by Laura1.7k
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