jvarkit

BamLiftOver

Lift-over a BAM file.

Usage

Usage: bamliftover [options] Files
  Options:
    --bamcompression
      Compression Level.
      Default: 5
    -f, --chain
      LiftOver file. Require
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -m, --minmatch
      lift over min-match. default:-1 == use default value from htsjdk 
      LiftOver.DEFAULT_LIFTOVER_MINMATCH 
      Default: -1.0
    -o, --output
      Output file. Optional . Default: stdout
    -D, -R, --reference
      indexed REFerence file for the new sequence dictionary. Required
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --version
      print version and exit

Keywords

• bam
• liftover

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew bamliftover

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/liftover/BamLiftOver.java

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite bamliftover ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

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