GTF2GFF(1)

NAME
gtf2gff.pl format convert a GTF file

SYNOPSIS
gtf2gff.pl <in.gtf --out=out.gff

    Besides easy by-line changes this script can in particular swap between the different representations of UTRs:
    a) explicit UTR lines (e.g. 3'-UTR or three_prime_utr)
    b) implicit specification by 'exon' and 'CDS' features

OPTIONS
  out                 gff output file
  --printExon         print exon features (may include CDS and UTR parts)
  --printUTR          print UTR features
  --printIntron       print intron features
  --gff3              output in gff3 format
  --includeStopInCDS  include stop codon in the CDS

DESCRIPTION
    example input:

    chr1 AUGUSTUS  gene        12656   14013   0.04    +   .   g50
    chr1 AUGUSTUS  transcript  12656   14013   0.04    +   .   g50.t1
    chr1 AUGUSTUS  tss         12656   12656   .       +   .   transcript_id "g50.t1"; gene_id "g50";
    chr1 AUGUSTUS  5'-UTR      12656   12867   0.2     +   .   transcript_id "g50.t1"; gene_id "g50";
    chr1 AUGUSTUS  start_codon 12868   12870   .       +   0   transcript_id "g50.t1"; gene_id "g50";
    chr1 AUGUSTUS  intron      12994   13248   1       +   .   transcript_id "g50.t1"; gene_id "g50";
    chr1 AUGUSTUS  CDS         12868   12993   0.8     +   0   transcript_id "g50.t1"; gene_id "g50";
    chr1 AUGUSTUS  CDS         13249   13479   1       +   0   transcript_id "g50.t1"; gene_id "g50";
    chr1 AUGUSTUS  stop_codon  13477   13479   .       +   0   transcript_id "g50.t1"; gene_id "g50";
    chr1 AUGUSTUS  3'-UTR      13480   14013   0.17    +   .   transcript_id "g50.t1"; gene_id "g50";
    chr1 AUGUSTUS  tts         14013   14013   .       +   .   transcript_id "g50.t1"; gene_id "g50";

    example output for --gff3 --printExon:

    chr1 AUGUSTUS  gene                     12656   14013   0.04    +   .   ID=g50;
    chr1 AUGUSTUS  mRNA                     12656   14013   0.04    +   .   ID=g50.t1;Parent=g50
    chr1 AUGUSTUS  transcription_start_site 12656   12656   .       +   .   Parent=g50.t1;
    chr1 AUGUSTUS  five_prime_utr           12656   12867   0.2     +   .   ID=g50.t1.5UTR1;Parent=g50.t1
    chr1 AUGUSTUS  exon                     12656   12993   .       +   .   ID=g50.t1.exon1;Parent=g50.t1;
    chr1 AUGUSTUS  start_codon              12868   12870   .       +   0   Parent=g50.t1;
    chr1 AUGUSTUS  CDS                      12868   12993   0.8     +   0   ID=g50.t1.CDS1;Parent=g50.t1
    chr1 AUGUSTUS  intron                   12994   13248   1       +   .   Parent=g50.t1;
    chr1 AUGUSTUS  CDS                      13249   13479   1       +   0   ID=g50.t1.CDS2;Parent=g50.t1
    chr1 AUGUSTUS  exon                     13249   14013   .       +   .   ID=g50.t1.exon2;Parent=g50.t1;
    chr1 AUGUSTUS  stop_codon               13477   13479   .       +   0   Parent=g50.t1;
    chr1 AUGUSTUS  three_prime_utr          13480   14013   0.17    +   .   ID=g50.t1.3UTR1;Parent=g50.t1
    chr1 AUGUSTUS  transcription_end_site   14013   14013   .       +   .   Parent=g50.t1;