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.
--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 \ --disableFail
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.
ValidateVcf 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 ValidateVcf. We have had
good results with this IDE.