jvarkit

KnownRetroCopy

Last commit

Annotate VCF structural variants that could be intron from retrocopies.

Usage

Usage: knownretrocopy [options] Files
  Options:
    -d, --distance
      max distance between an intron and the deletion found in the VCF
      Default: 10
  * -gtf, --gtf
      GTF file that was used by STAR
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -k, --known
      Gene-ID of known retrogenes. One per line. A source could be : 
      http://retrogenedb.amu.edu.pl/static/download/ 
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

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

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

Creation Date

2019-08-15

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/retrocopy/KnownRetroCopy.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/retrocopy/KnownRetroCopyTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite knownretrocopy ? 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