This tool repairs a broken GTF file that does not contain all genes and transcripts. A proper GTF file lists genes, transcripts and exons. However some tools only add exons to the GTF file. AddGenesAndTranscriptsToGtf adds genes and transcripts to a GTF file, based on the exons available in an input GTF file.


AddGenesAndTranscriptsToGtf requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.

Download the latest version of AddGenesAndTranscriptsToGtf here. To generate the usage run:

java -jar <AddGenesAndTranscriptsToGtf_jar> --help


AddGenesAndTranscriptsToGtf determines the genes and transcripts from the listed exons in the input GTF. Only an input and an output GTF need to be passed to the command line.


To create a GTF file with genes and transcripts from a GTF file with missing genes and transcripts:

java -jar <AddGenesAndTranscriptsToGtf_jar> \
-I input.gtf \
-o output.gtf


Usage for AddGenesAndTranscriptsToGtf:

Option Required Can occur multiple times Description
--log_level, -l no no Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
--help, -h no no Print usage
--version, -v no no Print version
--input, -I yes no Input gtf file. Mandatory
--output, -o yes no Output gtf file. Mandatory


AddGenesAndTranscriptsToGtf is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of BIOPET pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.


The source code of AddGenesAndTranscriptsToGtf can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

AddGenesAndTranscriptsToGtf is build using sbt. Before submitting a pull request, make sure all tests can be passed by running sbt test from the project's root. We recommend using an IDE to work on AddGenesAndTranscriptsToGtf. We have had good results with this IDE.


For any question related to AddGenesAndTranscriptsToGtf, please use the github issue tracker or contact the SASC team directly at: