jvarkit

MergeStructuralVariants

Experimental SV/CNV merger.

Usage

Usage: mergesv [options] Files
  Options:
    --bcf-output
      If this program writes a VCF to a file, The format is first guessed from 
      the file suffix. Otherwise, force BCF output. The current supported BCF 
      version is : 2.1 which is not compatible with bcftools/htslib (last 
      checked 2019-11-15)
      Default: false
    -d, --distance
      Two BND variants are the same if their bounds are distant by less than 
      xxx bases. A distance specified as a positive integer.Commas are 
      removed. The following suffixes are interpreted : b,bp,k,kb,m,mb,g,gb
      Default: 1
    -f, --fraction
      Two CNV/DEL/.. variants are the same if they share 'x' fraction of their 
      size. A decimal number between 0.0 and 1.0. If the value ends with '%' 
      it is interpretted as a percentage eg. '1%' => '0.01'. A slash '/' is 
      interpretted as a ratio. e.g: '1/100' => '0.01'.
      Default: 0.8
    --generate-vcf-md5
      Generate MD5 checksum for VCF output.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -m, --max-length
      ignore variant longer than 'x' bases. Ignore this parameter if 'x' <=0
      Default: -1
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• cnv
• indel
• sv

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 mergesv

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

Creation Date

20181109

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/structvar/MergeStructuralVariants.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/structvar/MergeStructuralVariantsTest.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 mergesv ? 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

About

Experimental SV/CNV merger.

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