jvarkit

VcfBurdenRscriptV

Last commit

Fisher Case / Controls per Variant (Vertical)

Usage

Usage: vcfburdenrscriptv [options] Files
  Options:
    --cadd, -cadd
      [20180831] Include CADD data, if available (INFO/CADD_PHRED 
      INFO/CADD_SCORE) 
      Default: false
    -cpm, --cadd-phred-missing
      [20180831] value for CADD / phred missing data
      Default: NA
    -csm, --cadd-score-missing
      [20180921] value for CADD / score missing data
      Default: NA
    -f, --function
      User defined R function to be called after each VCF
      Default: <empty string>
    -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
    -minusnineiszero, --minusnineiszero
      No Call is '0' (default is -9)
      Default: false
    --nfe
      [20180910] INCLUDE gnomad genome NFE AC
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -p, --pedigree
      [20180831] pedigree file (or I will try to extract the pedigree from 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
    -t, --title
      Try to find ##(TITLE)=abcdefghijk in the VCF header and use it as the 
      name of the VCF chunk
      Default: <empty string>
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

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

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/VcfBurdenRscriptV.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcfburdenrscriptv ? 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

Output

INFO column

FILTER column

see also

History