VcfBurdenSlidingWindow

apply fisher test on VCF using a sliding window

Usage

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

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

Usage: vcfburdenslidingwindow [options] Files
  Options:
    --cases
      File or comma-separated list of control samples
    -C, --contig
      limit to this contig
    --controls
      File or comma-separated list of control samples
    -f, --filter
      A Java EXpression Language (JEXL) expressions to filter the variants 
      from a VCF. Empty string will accept all variants. Expression returning 
      a TRUE will accept the variant. See 
      https://gatk.broadinstitute.org/hc/en-us/articles/360035891011 
      Default: <empty string> (ACCEPT ALL)
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -save-vcf, --save-vcf
      Save Matching variants for the best p-value into that VCF.
    -t, --treshold
      fisher-test treshold. Discard results greater than this value.
      Default: 1.0
    --version
      print version and exit
    -s, --window-shift
      Window shift
      Default: 300
    -w, --window-size
      Window size
      Default: 1000

Keywords

• vcf
• burden
• case
• control

Creation Date

20190920

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/burden/VcfBurdenSlidingWindowTest.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 vcfburdenslidingwindow ? 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

apply fisher test on VCF using a sliding window

Example

$ java -jar dist/jvarkit.jar vcfburdenslidingwindow --cases cases.txt --controls controls.txt -t 1 ./src/test/resources/test_vcf01.vcf  | head

#chrom  start0  end name    length  p-value affected_alt    affected_hom    unaffected_alt  unaffected_hom  variants.count
1   832199  833200  1:832200-833200 1001    1.0 0   3   1   2   1
1   832499  833500  1:832500-833500 1001    1.0 0   3   1   2   1
1   832799  833800  1:832800-833800 1001    1.0 0   3   1   2   1
1   839999  841000  1:840000-841000 1001    1.0 0   3   1   2   1
1   840299  841300  1:840300-841300 1001    1.0 0   3   1   2   1
1   840599  841600  1:840600-841600 1001    1.0 0   3   1   2   1
1   849299  850300  1:849300-850300 1001    1.0 0   3   1   2   1
1   849599  850600  1:849600-850600 1001    1.0 1   2   1   2   2
1   849899  850900  1:849900-850900 1001    1.0 1   2   1   2   2