jvarkit

VcfTrap

annotate vcf with trap database http://trap-score.org/

Usage

Usage: vcftrap [options] Files
  Options:
    -A, --attribute
      VCF INFO attribute Format:(ALT|GENE|SCORE)
      Default: TRAP
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --ignore-filtered
      Ignore FILTERed variants (faster)
      Default: false
  * -m, --manifest
      Manifest file. A tab delimited file with two columns : 
      chromosome(tab)path-to-file-indexed-with-trapindex. 
    -o, --out
      Output file. Optional . Default: stdout
    --outputbcf
      Output bcf (for streams)
      Default: false
    --vcfcreateindex
      VCF, create tribble or tabix Index when writing a VCF/BCF to a file.
      Default: false
    --vcfmd5
      VCF, create MD5 checksum when writing a VCF/BCF to a file.
      Default: false
    --version
      print version and exit

Keywords

• vcf
• trap
• 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 vcftrap

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/trap/VcfTrap.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 vcftrap ? 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/trapindexer.jar  -o chr22.dat chr22.TraPv2.txt.gz
echo -e "22\tchr22.dat" > out.manifest
java -jar dist/vcftrap.jar -m out.manifest input.vcf

See also

• TrapIndexer

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