Manhattan plot SVG picture from different sources.
Usage: java -jar dist/manhattan.jar [options] Files
Usage: manhattan [options] Files
Options:
--bed, -L
BED file containing one or more region to observe. Use the whole
chromosome if undefined
-D, --define
Dynamic parameters
Syntax: -Dkey=value
Default: {}
--dimension
Image Dimension. a dimension can be specified as '[integer]x[integer]'
or it can be the path to an existing png,jpg,xcf,svg file.
Default: java.awt.Dimension[width=1000,height=300]
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--include
include chromosomes matching the following expression
Default: (chr)?[0-9XY]+
-o, --output
Output file. Optional . Default: stdout
* -R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard CreateSequenceDictionary
--version
print version and exit
-l
List available handlers and exit
Default: false
-n
handler name
Default: default
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew manhattan
The java jar file will be installed in the dist
directory.
20220525
The project is licensed under the MIT license.
Should you cite manhattan ? 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