GtfToGff

Last commit

Convert GTF to gff

Usage

Usage: java -jar dist/gtf2gff.jar  [options] Files
Usage: gtf2gff [options] Files
  Options:
    --biotype
      Default biotype (empty:no default)
    --escape-UTF8
      escape UTF-8
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --make-gene
      When 'gene' is missing, create a gene for each 'transcript/mrna'
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

gtf
gff
gff3

Compilation

Requirements / Dependencies

java compiler SDK 17. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone --recurse-submodules "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew gtf2gff

The java jar file will be installed in the dist directory.

Creation Date

20220703

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/gtf/GtfToGff.java

Contribute

Issue Tracker: http://github.com/lindenb/jvarkit/issues
Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite gtf2gff ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030