jvarkit

VcfSkat

Calculate SKAT score for a VCF.

Usage

Usage: vcfskat [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -ped, --pedigree
      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  If not defined, I will try to extract the pedigree 
      from  the VCFheader.
    -p, --print
      Don't print the VCF on output,Just print the score on ouput, don't print 
      the VCF itself
      Default: false
    --skat-accept-filtered
      accept variants FILTER-ed
      Default: false
    --skat-adjusted
      SKAT adjusted
      Default: false
    --skat-num-retry
      compute n-times the p-value
      Default: 1
    --skat-optimized
      SKAT optimized (SKATO)/ davies method.
      Default: false
    --skat-random-seed
      Rstats value for `set.seed`. -1 == use random
      Default: -1
    -tag, --tag
      tag name in VCF header "tag=p-value"
      Default: SKAT
    --version
      print version and exit

Keywords

• vcf
• pedigree
• skat
• burden

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 vcfskat

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/skat/VcfSkat.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 vcfskat ? 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/vcfskat.jar vcf_with_samples.vcf | grep SKAT
##SKAT=0.2215079

$ java -jar dist/vcfskat.jar -p vcf_with_samples.vcf 
0.2215079

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