This tool converts a sample track within an XHMM XCNV file to a BED track. In the output the fourth column indicates the type of CNV for the region: deletion (-1), normal (0) or duplication (1).
XcnvToBed 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 XcnvToBed here. To generate the usage run:
java -jar <XcnvToBed_jar> --helpThis tool converts a sample track within an XHMM XCNV file to a BED track. In the output the fourth column indicates the type of CNV for the region: deletion (-1), normal (0) or duplication (1).
java -jar <XcnvToBed_jar> \
-I input.xcnv \
-O output.bed \
-S sampleSpecify in sample which sample should be extracted to the BED file.
Usage for XcnvToBed:
| 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 XCNV file |
| --Output, -O | yes | no | Output BED file |
| --Sample, -S | yes | no | The sample which to select |
XcnvToBed 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 XcnvToBed can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.
XcnvToBed 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 XcnvToBed. We have had
good results with this IDE.
For any question related to XcnvToBed, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.