jvarkit

VcfBurden

Solena: vcf to (chrom/pos/ref/alt/individus(G:0/1/2/-9)

DEPRECATED

deprecated

Usage

Usage: vcfburden [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      zip file
    --version
      print version and exit
    -H
       only high damage
      Default: false
    -d
       (dir) base zip dir
      Default: burden
    -f
       print ALL consequence+ colum, SO terms (mail matilde 11/10/2015 11:38 
      AM) 
      Default: false
    -g
       (file) optional list of gene names (restrict genes, print genes without 
      data) 
    -p
       print position in CDS
      Default: false
    -q
       print VQSLOD
      Default: false

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 vcfburden

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/misc/VcfBurden.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 vcfburden ? 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

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