Plot a Hilbert Curve from a VCF file.
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
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcf2hilbert
The java jar file will be installed in the dist
directory.
The project is licensed under the MIT license.
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