GtftoRefflat converts a GTF file to a refflat file.


GtftoRefflat 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 GtftoRefflat here. To generate the usage run:

java -jar <GtftoRefflat_jar> --help


GtftoRefflat converts a GTF file to a refflat file. It can optionally use a reference FASTA file to check if all contigs are present on this reference FASTA file.


To convert a gtf to refflat and check if all contigs are present in the reference:

java -jar <GtftoRefflat_jar> \
-g input.gtf \
-r output.refflat \
-R reference.fa


Usage for GtftoRefflat:

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
--refFlat, -r yes no Output refFlat file. Mandatory
--gtfFile, -g yes no Input gtf file. Mandatory
--referenceFasta, -R no no Reference file


GtftoRefflat 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.

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


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

GtftoRefflat 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 GtftoRefflat. We have had good results with this IDE.


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