Converting VCF to GFF (again)

[francois.sabot]

Hi folks,
I know the question was already asked here (as in http://seqanswers.com/forums/showthr...hlight=gff+vcf)..

But my problem is that the data I have are on plants, and are massive... I mean, I have performed a GATK SNP calling for ALL sites, including indel, and the final file is of 49Go (VCF).

My aim is to convert it to GFF, and in this GFF to include the large deletions (missing regions in queries either from non-existing sequence or from technical aspects) as well as the small SNP and indel. Moreover I would like to conserve the RG infos as I have multiple samples in the VCF

I wonder if someon already starts working on something like that ?

Thanks

Francois

[giorgifm]

I have the same problem, and unfortunately I see you didn't have much luck in finding an answer... How did you fix it?

[danwiththeplan]

still a problem?

Is this still a problem for anyone? I wrote a very simple script to convert .vcf to .gff3 format, it has not been tested, but you could try it and modify it for your own use if you want.

[floem7]

If you still have it, please provide it.