ValidateAnnotationvalidates whether an annotation file is correct. It checks whether all the annotated contigs are present on the reference. It can check gtf or refflat files. It can also check both, in which case it will also check for dissimilarities between the refflat and GTF files.


ValidateAnnotation 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 ValidateAnnotation here. To generate the usage run:

java -jar <ValidateAnnotation_jar> --help


ValidateAnnotation requires either a refflatfile or a GTF file. It also requires a reference genome to check the annotation. reference genome to check the annotation.

The tool has a --disableFail flag which makes sure the tool returns exit code 0 when the tool has failed.


ValidateAnnotation can accept both a refflat File and a GTF file:

java -jar <ValidateAnnotation_jar> \
-r refflatFile \
-g gtfFile1 \
-R reference.fasta

Running the validation on only one of them is also possible:

java -jar <ValidateAnnotation_jar> \
-r refflatFile \
-R reference.fasta


Usage for ValidateAnnotation:

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
--refflatFile, -r no no Refflat file to check
--gtfFile, -g no no Gtf files to check
--reference, -R yes no Reference fasta to check vcf file against
--disableFail no no Do not fail on error. The tool will still exit when encountering an error, but will do so with exit code 0


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

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


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