Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Is there a tool that converts TXT, BED, GFF format to VCF? LauraSmith Bioinformatics 4 03-22-2017 02:41 AM
Converting VCF to GFF (again) francois.sabot Bioinformatics 3 08-24-2016 04:48 AM
Annotation: Glimmer to GFF Daniel Fernandez Bioinformatics 1 08-08-2014 01:00 AM
GFF Annotation file AAWT Bioinformatics 3 12-12-2012 12:58 AM
need help with converting VCF to GTF/GFF format rudi283 Bioinformatics 4 03-05-2011 11:49 AM

Thread Tools
Old 10-18-2012, 06:55 AM   #1
Location: Columbia University Medical Center

Join Date: Aug 2011
Posts: 35
Default 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

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!
giorgifm is offline   Reply With Quote
Old 08-10-2013, 09:56 AM   #2
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?
lukas1848 is offline   Reply With Quote
Old 08-11-2013, 04:09 AM   #3
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.
dpryan is offline   Reply With Quote
Old 09-05-2013, 06:09 PM   #4
Junior Member
Location: New York

Join Date: Aug 2013
Posts: 4

I also have the same issue - did anyone find a solution?
r_j_p is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:42 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO