VcfToRScript

Last commit

Convert VCF to R so it can be used for burden testing

Usage

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

Usage: java -jar dist/jvarkit.jar vcf2r  [options] Files

Usage: vcf2r [options] Files
  Options:
    --cases
      File or comma-separated list of control samples
    --controls
      File or comma-separated list of control samples
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --info
      comma separated of extra INFO fields included in the variant dataframe. 
      Only with --variants
      Default: <empty string>
    -o, --output
      Output file. Optional . Default: stdout
    --variants
      include a table with variants
      Default: false
    --version
      print version and exit

Keywords

vcf
burden
fisher
R

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcf2r/VcfToRScript.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 vcf2r ? 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