GFF annotation converted to a new GFF based on VCF information

[giorgifm]

Dear all,

I am producing a VCF file on a (inbred) variety vs. the reference, for which I have a nice GFF3-formatted annotation.
Starting from reads and alignments, I can produce the VCF (via the GATK Hapolotype caller and various recalibration steps), by which I created a new variety-specific fasta via the GATK FastaAlternateReference command

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_fasta_FastaAlternateReference.html

However, due to indels, the GFF3 coordinates are all screwed up. Therefore I would like to generate a new GFF3 for the alternate reference, based on the VCF-contained variant information.

Do you guys have any clue if such a tool exist? Or alternatively, if I should use a different pipeline altogether.

Thanks a lot!

[lukas1848]

I am looking for an answer to the exact same question, so I'm bumping this thread. Is anyone aware of a script that can change a gff file with respect to InDels?

[dpryan]

You might just write a script to convert the VCF file to a format accepted by liftOver and then run it on the gff file. Keep in mind that some intron-exon boundaries may be wrong after this.

A caveat about converting GFF files is described here.

[r_j_p]

I also have the same issue - did anyone find a solution?