jvarkit

VcfStats

Produce VCF statitics

Usage

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

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

Usage: vcfstats [options] Files
  Options:
    --fill-group
      assign group 'x' to sample if it's not defined in the file for 
      --categories. Special value = '*' : assign the sample name to it's own 
      private group
      Default: other
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --list, -l
      list available modules and exit
  * -o, --output
      Output directory
    --prefix
      file prefix
      Default: <empty string>
    --title
      title as prefix
      Default: <empty string>
    --version
      print version and exit

Keywords

• vcf
• stats
• R

Creation Date

20131212

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfstats/VcfStats.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/vcfstats/VcfStatsTest.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 vcfstats ? 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/jvarkit.jar vcfstats src/test/resources/rotavirus_rf.unifiedgenotyper.vcf.gz |  R --no-save 

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