This tool merges a VCF file with another VCF file. It provides several options on how to merge INFO fields with the same name.
VcfWithVcf 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 VcfWithVcf here. To generate the usage run:
java -jar <VcfWithVcf_jar> --help
VcfWithVcf requires an input VCF, secondary input VCF, output VCF and a reference genome fasta. It has opptions to merge fileds with the field flag -f.
In order to combine input.vcf with secondary.vcf run the following command:
java -jar <VcfWithVcf_jar> \ -I input.vcf \ -s secondary.vcf \ -R reference.fa \ -o \ -output.vcf
Usage for VcfWithVcf:
|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|
|--inputFile, -I||yes||no||Input VCF file|
|--secondaryVcf, -s||no||no||Second Input VCF file|
|--outputFile, -o||yes||no||Output VCF file.|
|--reference, -R||yes||no||The refence that was used to call the VCF|
|--field, -f||no||yes (unlimited)|| If only
|--match||no||no||Match alternative alleles; default true|
VcfWithVcf 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.
VcfWithVcf 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 VcfWithVcf. We have had
good results with this IDE.