jvarkit

VcfBurdenFisherV

Last commit

Fisher Case / Controls per Variant (Vertical)

Usage

Usage: vcfburdenfisherv [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -if, --ignorefilter
      accept variants having a FILTER column. Default is ignore variants with 
      a FILTER column
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -p, --pedigree
      [20190121] Pedigree file. Default: use the pedigree data in the VCF 
      header.A pedigree is a text file delimited with tabs. No header. Columns 
      are (1) Family (2) Individual-ID (3) Father Id or '0' (4) Mother Id or 
      '0' (5) Sex : 1 male/2 female / 0 unknown (6) Status : 0 unaffected, 1 
      affected,-9 unknown
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

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

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

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/burden/VcfBurdenFisherV.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfburdenfisherv ? 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

Variant in that VCF should have one and only one ALT allele. Use https://github.com/lindenb/jvarkit/wiki/VcfMultiToOneAllele if needed.

Output

INFO column

FILTER column

see also