jvarkit

ReferenceToVCF

Creates a VCF containing all the possible substitutions from a Reference Genome.

Usage

Usage: referencetovcf [options] Files
  Options:
    -L, --bed
      limit to this BED
    -d, --deletions
      generate deletions
      Default: 0
    -A, --disjoint
      disjoint ALT
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -i, --insertions
      generate insertions
      Default: 0
    -o, --output
      Output file. Optional . Default: stdout
    --version
      print version and exit

Keywords

• vcf
• reference
• fasta

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 referencetovcf

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/ReferenceToVCF.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 referencetovcf ? 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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