This tool will merge structural variants from different callers and different samples. Because SV's are not always exact on base resolution called the merging must be done within the windows what the callers say the SV's is placed.


MergeSv 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 MergeSv here. To generate the usage run:

java -jar <MergeSv_jar> --help


Each file can be tagged with a key, this can be used to see which callers does call the same event. By default it try to stay withing the confident range the caller did specify.


Sample ID's in the input files should be correct, this is used in merging.

Default example:

java -jar <MergeSv_jar> \
-R <reference_fasta> \
-i <caller>=<input_file> \
-i <caller>=<input_file> \
-o <output_file>


Usage for MergeSv:

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 yes (unlimited) Input vcf files to merge into a single file
--outputFile, -o yes no Output vcf file
--referenceFasta, -R yes no Reference fasta file
--windowsSize no no Size of sliding window, default is 1000 basepair
--defaultCi no no Interval when caller does not give one, default is 75 basepair
--keepNonVariant no no By default calls without a genotype with a alternative allele will be filtered. This option keeps them in the merging.
--callerField no yes (unlimited) Format fields to copy to new vcf file.


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

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


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