jvarkit

VcfBurdenFisherH

Last commit

Fisher Case /Controls per Variant

Usage

Usage: vcfburdenfisherh [options] Files
  Options:
    --attribute
      [20190418] Name of the attribue used as FILTER and INFO
      Default: BurdenHFisher
    -gtf, --gtf, --gtFiltered
      [20180115] Ignore FILTERed **Genotype**
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -ignoreFiltered, --ignoreFiltered
      [20171031] Don't try to calculate things why variants already FILTERed 
      (faster) 
      Default: false
    -lumpy-su-min, --lumpy-su-min
      [20180115] if variant identified as LUMPy-SV variant. This is the 
      minimal number of 'SU' to consider the genotype as a variant.
      Default: 1
    -fisher, --minFisherPValue
      if p-value fisher(case/control vs have alt/have not alt) lower than 
      'fisher' the FILTER Column is Filled
      Default: 0.05
    -o, --output
      Output file. Optional . Default: stdout
    -p, --pedigree
      [20180115] 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
    --report
      [20190418] save report as bed file
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

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

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/VcfBurdenFisherH.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/burden/VcfBurdenFisherHTest.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfburdenfisherh ? 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

Input

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

VCF header must contain a pedigree ( see VCFinjectPedigree ) or a pedigree must be defined.

Lumpy-SV

see also