GFF annotation converted to a new GFF based on VCF information

giorgifm · 10-18-2012, 06:55 AM

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/g...Reference.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 · 08-10-2013, 09:56 AM

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 · 08-11-2013, 04:09 AM

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 · 09-05-2013, 06:09 PM

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

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10-18-2012, 06:55 AM	#1
giorgifm Member Location: Columbia University Medical Center Join Date: Aug 2011 Posts: 35	GFF annotation converted to a new GFF based on VCF information 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/g...Reference.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!

08-11-2013, 04:09 AM	#3
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	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. Last edited by dpryan; 08-11-2013 at 04:51 AM.

08-10-2013, 09:56 AM	#2
lukas1848 Member Location: Germany Join Date: Jun 2011 Posts: 54	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?

09-05-2013, 06:09 PM	#4
r_j_p Junior Member Location: New York Join Date: Aug 2013 Posts: 4	I also have the same issue - did anyone find a solution?