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