jvarkit

VcfAnnotWithBeacon

Annotate a VCF with ga4gh beacon

Usage

Usage: vcfannotwithbeacon [options] Files
  Options:
    --baseurl
      Beacon Base URL API
      Default: https://beacon-network.org/api
    -B, --bdb
      Optional BerkeleyDB directory to store result. Avoid to make the same 
      calls to beacon
    --build
      genome build
      Default: HG19
    --cert
      ignore SSL certification errors
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --noupdate
      Don't query the variant already having the tag / do not update the 
      existing annotation
      Default: false
    -o, --out
      Output file. Optional . Default: stdout
    --stopOnError
      Stop on network error.
      Default: false
    --tag, -T
      INFO TAG
      Default: BEACON
    --tee
      show what's happening in the network
      Default: false
    --version
      print version and exit

Keywords

• ga4gh
• beacon
• vcf
• annotation

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 vcfannotwithbeacon

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/ga4gh/VcfAnnotWithBeacon.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/ga4gh/VcfAnnotWithBeaconTest.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 vcfannotwithbeacon ? 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

This site is open source. Improve this page.