jvarkit

VcfBraiding

Last commit

visualization for variants and attributes using https://visdunneright.github.io/sequence_braiding/docs/ .

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar vcfbraiding  [options] Files

Usage: vcfbraiding [options] Files
  Options:
    --alleles
      show alleles in header.
      Default: false
    -B, --base
      Base URL for code 
      :https://visdunneright.github.io/sequence_braiding/docs/ 
      Default: https://visdunneright.github.io/sequence_braiding/docs/
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --hom-ref, -hr
      remove sample that are all HOM_REF for all variants.
      Default: false
    --id
      id for svg element.
      Default: vcfid
    --no-call, -nc
      remove sample that are all NO_CALL for all variants.
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -T, --title
      title
      Default: <empty string>
    --version
      print version and exit
    -D
      Dynamic parameters for API 'options'. -Dkey=value . Keys are currently: 
      show_seq_names forceLevelName animate  colorbysequence width height 
      fontSize padding.
      Syntax: -Dkey=value
      Default: {}

Keywords

Creation Date

20201021

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/braiding/VcfBraiding.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfbraiding ? 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

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