jvarkit

CaseControlJfx

chart of case/control maf from a VCF and a pedigree

Usage

Usage: casectrljfx [options] Files
  Options:
    -filter, --filter
      Ignore FILTERed variants
      Default: false
    -gtfilter, --genotypefilter
      Ignore FILTERed Genotypes
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --limit
      Limit to 'N' variants. negative==no limit; All point are loaded in 
      memory. The more variants you have, the more your need memory
      Default: -1
    -mafTag, --mafTag
      [20180905] Do not calculate MAF for controls, but use this tag to get 
      Controls' MAF. How to extract the AlleleFrequencies from a variant. 
      Multiple separated with comma or semicolon. e.g: 
      "AC/AN;exome_CEU_*;genome_NFE_AF;another_AC/another/AN". Input is a set 
      of AC/AN field pairs or/and AF field separated by semicolon. 'x/y' means 
      AC/AN fields. '*' will be replaced with AC and AN, hence, 'exome_CEU_*' 
      will be interpreted as exome_CEU_AC/exome_CEU_AN. Other field will be 
      interpreted as an AF field.
    -nchr, --nocallishomref
      treat no call as HomRef
      Default: false
    --opacity
      Point opaciy [0-1]
      Default: 0.4
    -o, --out
      Save the image in a file and then exit.
    -partition, --partition
      partition type. How series are built. For example 'variantType' will 
      produces some series for INDEL, SNP, etc...
      Default: variantType
      Possible Values: [chromosome, variantType, autosomes, qual, vqslod, typeFilter, distance, n_alts]
    -p, --ped, --pedigree
      Pedigree File. If not defined, try to use the pedigree inserted in the 
      VCF header.
    --sex
      Select/Filter samples on their gender.
      Default: all
      Possible Values: [all, males, females]
    --title
      Default title for the graph
    --version
      print version and exit

Keywords

• vcf
• pedigree
• case
• control
• visualization
• jfx
• chart
• maf

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

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

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/CaseControlJfx.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 casectrljfx ? 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/casectrljfx.jar --pedigree  mutations.ped mutations.vcf

See also:

• https://twitter.com/yokofakun/status/860495863633805312

screenshot

History

• removed JFX because openjdk doesn’t support JFX

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