jvarkit
VcfToPostscript
Print VCF context as Postscript
Usage
Usage: vcf2postscript [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-kg, -k, --knownGene
UCSC knownGene File/URL. The knowGene format is a compact alternative to
GFF/GTF because one transcript is described using only one line. Beware
chromosome names are formatted the same as your REFERENCE. A typical
KnownGene file is
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz
.If you only have a gff file, you can try to generate a knownGene file
with [http://lindenb.github.io/jvarkit/Gff2KnownGene.html](http://lindenb.github.io/jvarkit/Gff2KnownGene.html)
Default: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz
-o, --out
Output file. Optional . Default: stdout
--version
print version and exit
Keywords
- vcf
- postscript
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 vcf2postscript
The java jar file will be installed in the dist directory.
Source code
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 vcf2postscript ? 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