jvarkit

VcfBurdenFilterExac

Last commit

Burden filter 3 - Exac

Usage

Usage: vcfburdenexac [options] Files
  Options:
    -d, --discardNotInExac
      if variant was not found in Exac, set the FILTER. Default: don't set the 
      FILTER. 
      Default: false
  * -exac, --exac
      Path to Exac VCF file. At the time of writing, you'd better use a 
      normalized version of Exac (see 
      https://github.com/lindenb/jvarkit/wiki/VCFFixIndels )
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -maxFreq, --maxFreq
      set FILTER if max(exac frequency in any pop) is greater than this value)
      Default: 0.001
    -o, --output
      Output file. Optional . Default: stdout
    -pop, --population
      comma separated populations in exac
      Default: AFR,AMR,EAS,FIN,NFE,SAS
    -tabix, --tabix
      use tabix index for Exac it is present. Might speed up things if the 
      number of variant is low.
      Default: false
    --version
      print version and exit

Keywords

vcf
burden
exac

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 vcfburdenexac

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/VcfBurdenFilterExac.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 vcfburdenexac ? 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

20170626: this tool now supports multiple ALT in the user VCF, however it’s not been tested for choosing when to set the FILTER or the min value