Lift-over a BAM file.
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
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew bamliftover
The java jar file will be installed in the dist
directory.
The project is licensed under the MIT license.
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