jvarkit

SwingVcfView

VCFviewer using Java Swing UI

Usage

Usage: java -jar dist/swingvcfview.jar  [options] Files
Usage: swingvcfview [options] Files
  Options:
    --gff, --gff3
      GFF3 file Path used to find intervals by gene name
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -r, --regions, --interval
      default interval region on opening
      Default: <empty string>
    --limit
      Limit number of variants. Ignore if < 0
      Default: -1
    --pedigree
      A pedigree file. tab delimited. Columns: family,id,father,mother, 
      sex:(0:unknown;1|male|M:male;2|female|F:female), phenotype 
      (-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected) 
    --version
      print version and exit

Keywords

• vcf
• visualization
• swing

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 swingvcfview

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

Creation Date

20210503

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfviewgui/SwingVcfView.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 swingvcfview ? 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/swingvcfview.jar input.vcf.gz

Screenshot

• https://twitter.com/yokofakun/status/1392173413079322625

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