ExtractTagsFromGtf extracts tags from a GTF refflat file and outputs the results in tsv format.


ExtractTagsFromGtf 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 ExtractTagsFromGtf here. To generate the usage run:

java -jar <ExtractTagsFromGtf_jar> --help


ExtractTagsFromGtf can select tags from a refflat file and optionally filter for a specific feature. The number of tags that can be selected is unlimited, at least one tag is required.


To extract tag1, tag2 and tag3 from inputRefflat and filter only for feature type feature:

java -jar <ExtractTagsFromGtf_jar> \
-i inputRefflat \
-o output.tsv \
-t tag1 \
-t tag2 \
-t tag3 \
-f feature


Usage for ExtractTagsFromGtf:

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
--gtfFile, -i yes no Input gtf file. Mandatory
--output, -o yes no Output tsv file. Mandatory
--tag, -t yes yes (unlimited) Tags to extract
--feature, -f no no Filter for only this feature type
--addPositions no no Add positions to output


ExtractTagsFromGtf 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 ExtractTagsFromGtf can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

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


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