ValidateVcf validates a VCF file against a reference genomes. It checks if the positions present in the VCF are also present on the reference genoome.


ValidateVcf 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 ValidateVcf here. To generate the usage run:

java -jar <ValidateVcf_jar> --help


To run this tool a vcf file and a reference genome are needed. Optionally, a --disableFail flag can be set. This will make the tool always exit with exit code 0.


To validate a vcf file against a reference genome use:

java -jar <ValidateVcf_jar> \
-i input.vcf \
-R myReference.fa

To validate but not fail on exit use:

java -jar <ValidateVcf_jar> \
-i input.vcf \
-R myReference.fa \


Usage for ValidateVcf:

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
--inputVcf, -i yes no Vcf file 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


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

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


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