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