jvarkit

OptimizeFisher

Optimize fisher test on VCF using genetic algo

Usage

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

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

Usage: optimizefisher [options] Files
  Options:
    --cases
      File or comma-separated list of control samples
    --chiasma
      Proba chiasma
      Default: 0.01
    --controls
      File or comma-separated list of control samples
    --disable
      disable factory(ies) by name. Comma separated
      Default: <empty string>
    --duration
      format: <integer>(years|week|days|hours|minutes|seconds)
      Default: 23h
    --gtf
      tabix indexed gtf file for context drawing
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --max-variants-per-solution
      Maximum number of variants per solution.
      Default: 3000000000
    --max-window-size
      max sliding window side
      Default: 100000
    --min-window-size
      min sliding window side
      Default: 100
    --mutation
      Proba mutation
      Default: 0.01
    --n-samples-per-generation, -nsg
      Number of samples per generation.
      Default: 5
  * --output, -o
      Output directory
    --roi
      ROI regions of interesets as a BED file chrom/start/end/ROI-NAME . 
      Multiple interval can be defined for the same ROI-NAME. Use the whole 
      contig if undefined
    --threads
      number of threads
      Default: 1
    --version
      print version and exit

Keywords

• vcf
• burden
• fisher

Creation Date

20221013

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/burden/OptimizeFisher.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 optimizefisher ? 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

Motivation

loads a (small) VCF and memory and, using a genetic-algorithm, tries, to find the best set of parameters, the best genomic window to find the lowest FisherTest for a burden test.

Example

java -jar TMP/jvarkit.jar optimizefisher --cases TMP/cases.txt --controls TMP/ctrls.txt -o TMP TMP/normalized.vcf.gz

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