jvarkit

VcfBraiding

Last commit

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

Usage

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

Compilation

Requirements / Dependencies

Download and Compile

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

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

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

Example

bcftools view src/test/resources/rotavirus_rf.vcf.gz "RF02" "RF03" |\
	java -jar /home/lindenb/src/jvarkit-git/dist/vcfbraiding.jar --title "Rotavirus Variants" > variants.html

Screenshots

https://twitter.com/yokofakun/status/1319221221611941889

https://twitter.com/yokofakun/status/1319221221611941889

https://twitter.com/yokofakun/status/1319228442043387905

https://twitter.com/yokofakun/status/1319228442043387905

## See also: