jvarkit

CombineVcfFisher

Combine multiple VCF to perform a ‘vertical’ fisher test.

Usage

Usage: combinevcffisher [options] Files
  Options:
    --buffer
      buffer all genes/vcf in memory. Avoid to read each VCF twice or more but 
      consummes mmemory.
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --line
      switch to 'line' mode. Default is 'list' mode. See doc
      Default: false
    --max-fisher
      max fisher value to be printed.
      Default: 1.0
    -o, --output
      Output file. Optional . Default: stdout
  * -p, --pedigree
      A pedigree file. tab delimited. Columns: family,id,father,mother, 
      sex:(0:unknown;1:male;2:female), phenotype 
      (-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected) 
    --recursion
      pool size in 'list mode'. 1, 2 or 3.
      Default: 2
    --version
      print version and exit

Keywords

• vcf
• burden
• fisher

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 combinevcffisher

The java jar file will be installed in the dist directory.

Creation Date

20200910

Source code

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

input is a tab delimited text file with the list of paths to the indexed VCF files.

List mode

All vcf are stored in a list and we run the all combinations of ‘recursion’ VCFs.

Line mode

all the VCFs on the line are combined and tested.

Example

$ find dir -type f -name "*.vcf.gz" > paths.txt
$ java -jar ${JVARKIT_HOME}/dist/combinevcffisher.jar --buffer -p the.ped paths.txt

#genes        n-variants      cases-R cases-A controls-R      controls-A      fisher
G1:G2 13      238     4       90      10      0.0010580863010766208
G1:G3 6       241     1       94      6       0.0029829802538355616
G1:G4 6       241     1       94      6       0.0029829802538355616
G1:G5 6       241     1       94      6       0.0029829802538355616
G2:G3 6       241     1       94      6       0.0029829802538355616
G2:G4 6       241     1       94      6       0.0029829802538355616
G2:G5 6       241     1       94      6       0.0029829802538355616
G3:G4 6       241     1       94      6       0.0029829802538355616

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