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  • 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!

  • #2
    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?

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    • #3
      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, 03:51 AM.

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      • #4
        I also have the same issue - did anyone find a solution?

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