Produce VCF statitics
This program is now part of the main jvarkit
tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar vcfstats [options] Files
Usage: vcfstats [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--list
list available modules and exit
-o, --output
Output file. Optional . Default: stdout
--prefix
file prefix
Default: <empty string>
--version
print version and exit
-D
other parameters.
Syntax: -Dkey=value
Default: {}
20131212
The project is licensed under the MIT license.
Should you cite vcfstats ? 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
java -jar dist/jvarkit.jar vcfstats src/test/resources/rotavirus_rf.unifiedgenotyper.vcf.gz | R --no-save