DragenBndToInversion

Converts Dragen BND to inversions

Usage

Usage: java -jar dist/dragenbnd2inv.jar  [options] Files
Usage: dragenbnd2inv [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
    --emit-original
      emit original BND variants that makes an NV
      Default: false
    --emit-other
      write other variants that are not identified as BND/INV
      Default: false
    --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].
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• vcf
• dragen
• inversion
• bnd
• sv

Compilation

Requirements / Dependencies

• java compiler SDK 17. 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 --recurse-submodules "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew dragenbnd2inv

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

Creation Date

20241016

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/drageninv/DragenBndToInversion.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 dragenbnd2inv ? 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

Motivation

Dragen has no VCF with SVTYPE=INV

https://jp.support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/SW/Informatics/Dragen/MantaInversions_fDG.htm

Inversions are reported as a set of breakends. For example, given a simple reciprocal inversion, four breakends are reported, sharing the same EVENT INFO tag. The following is an example breakend records representing a simple reciprocal inversion: