This tool can be used to downsample specific regions. Each region can have it own fraction to downsample.
All other reads will not be touched.
DownsampleRegions 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 DownsampleRegions here. To generate the usage run:
java -jar <DownsampleRegions_jar> --help
To run this tool a bam file and a bed file is required. The bed file should be formatted like this:
By setting --deviation the fraction can deviate from it randomly.
Single end example:
java -jar
Paired end example:
java -jar
Usage for DownsampleRegions:
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 |
--bamFile, -b | yes | no | Input bam file |
--bedFile, -L | yes | no | Input bed file. 4e column defined the fraction |
--inputR1 | yes | no | Input R1 fastq |
--inputR2 | no | no | Input R2 fastq |
--outputR1A | yes | no | Output R1 fastq |
--outputR2A | no | no | Output R2 fastq |
--outputR1B | yes | no | Output R1 fastq |
--outputR2B | no | no | Output R2 fastq |
--deviation | no | no | Deviation of fractions |
--seed | no | no | Random seed |
DownsampleRegions 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 DownsampleRegions can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.
DownsampleRegions 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 DownsampleRegions. We have had
good results with this IDE.
For any question related to DownsampleRegions, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.