For a given set of BAM files, this tool calculates the the coverage for this set of BAM files together. It outputs the coverage per region.


MultiCoverage 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 MultiCoverage here. To generate the usage run:

java -jar <MultiCoverage_jar> --help


A bed file is needed for the regions. An unlimited number of BAM files can be submitted. The output is a tab seperated file that contains the coverage per region.


To check how much is covered by one.bam and another.bam together:

java -jar <MultiCoverage_jar> \
-L regions.bed \
-b one.bam \
-b another.bam \
-o output.txt


Usage for MultiCoverage:

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
--bedFile, -L yes no input bedfile
--bamFile, -b yes yes (unlimited) input bam files
--output, -o yes no output file
--mean no no By default total bases is outputed, enable this option make the output relative to region length


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

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


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