jvarkit

VcfToHilbert

Plot a Hilbert Curve from a VCF file.

Usage

Usage: vcf2hilbert [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    -r, --radius
      Radius Size
      Default: 3.0
    --version
      print version and exit
    -w, --width
      Image width
      Default: 1000

Keywords

• vcf
• image
• visualization

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 vcf2hilbert

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/hilbert/VcfToHilbert.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 vcf2hilbert ? 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

$  curl -s "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20140123_NA12878_Illumina_Platinum/NA12878.wgs.illumina_platinum.20140404.snps_v2.vcf.gz" | gunzip -c |\
 java -jar dist/vcf2hilbert.jar  -r 1.1 -w 1000 -o hilbert.png

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