Squishbed makes a BED file smaller by removing bases that are in overlapping records. Squishbed will report the number of bases before and after squishing.


SquishBed 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 SquishBed here. To generate the usage run:

java -jar <SquishBed_jar> --help


Squishbed requires a BED file as input. When squishing it can take the strand column into account with --strandSensitive and the name column with --nameSensitive.


The following example will create a squished BED file where the strand and name column have been taken into account:

java -jar <SquishBed_jar> \
-i myBED.bed \
-o mySquishedBED.bed \
--strandSensitive \

An example when running SquishBed


chrom chromstart chromend
ChrQ 0 10
ChrQ 5 15
ChrQ 10 20
ChrQ 25 35
ChrQ 50 80
ChrQ 60 70


chrom chromstart chromend
ChrQ 0 5
ChrQ 15 20
ChrQ 25 35
ChrQ 50 60
ChrQ 70 80


Usage for SquishBed:

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
--input, -i yes no Input BED file
--output, -o yes no Output BED file
--strandSensitive, -s no no Take strand column into account
--nameSensitive, -n no no Take name column into account


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

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


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