This tool makes a bed file with the positions from the input GVCF file. It selects the regions of a certain genome quality treshold.


GvcfToBed 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 GvcfToBed here. To generate the usage run:

java -jar <GvcfToBed_jar> --help


GvcfToBed needs an inputVcf and outputs to a bed file. Genome quality threshold can be set by the --minGenomeQuality flag. It can optionally output a inverted BED file.


To make a bed file from input.gvcf by taking sample F.catus-43 and output to output.bed:

java -jar <GvcfToBed_jar> \
-I input.gvcf \
-O output.bed \
-S F.catus-43


Usage for GvcfToBed:

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 Input vcf file
--outputBed, -O yes no Output bed file
--invertedOutputBed no no Output bed file
--sample, -S no no Sample to consider. Will take first sample on alphabetical order by default
--minGenomeQuality no no Minimum genome quality to consider


GvcfToBed 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 a pipeline, for example the SASC team's biowdl pipelines.

All tools in the BIOPET tool suite are Free/Libre and Open Source Software.


The source code of GvcfToBed can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.

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


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