RefflatStats generates stats about an annotation refflat file. It outputs stats files on genes, transcripts, exons and introns. Information includes start,end information, GC content, number of exonic regions etc.


RefflatStats 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 RefflatStats here. To generate the usage run:

java -jar <RefflatStats_jar> --help


RefflatStats requires the refflat file and an indexed reference fasta to run. If the reference is in reference.fa then a reference.fai and a reference.dict must also be present.


To output information on genes, transcripts, exons and introns:

java -jar <RefflatStats_jar> \
-a MouseAnnotation.refflat \
-R IndexedMouseReference.fa \
-g GeneOutput.tsv \
-t TranscriptOutput.tsv \
-e ExonOutput.tsv \
-i IntronOutput.tsv


Usage for RefflatStats:

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
--annotationRefflat, -a yes no The refflat file used for annotation
--referenceFasta, -R yes no The reference fasta file
--geneOutput, -g yes no Ouput file for genes
--transcriptOutput, -t yes no Output file for transcripts
--exonOutput, -e yes no Output file for exons
--intronOutput, -i yes no Output file for introns


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

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


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