jvarkit

LumpyVcfToCircos

Lumpy to Circos

Usage

Usage: lumpyvcf2circos [options] Files
  Options:
    -bnb, -bnd, --bnd
      hide SVTYPE=BND
      Default: false
    -del, --del, --deletions
      hide <DEL>
      Default: false
    -dup, --dup, --duplications
      hide <DUP>
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -inv, --inv, --invertions
      hide <INV>
      Default: false
    --su, --minsu
      Min supporting reads.
      Default: 20
    -o, --output
      output directory or zip file
    -p, --prefix
      file prefix
      Default: lumpy.
    --version
      print version and exit

Keywords

• lumpy
• circos
• sv
• vcf

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 lumpyvcf2circos

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/lumpysv/LumpyVcfToCircos.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 lumpyvcf2circos ? 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

Example

 java -jar dist/lumpyvcf2circos.jar  --minsu 50 -inv -bnb -dup  -o tmp  LumpyExpress.vcf.gz \
  && (cd tmp; /path/to/bin/circos  -outputdir . -conf lumpy.circos.conf  )

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