VCFviewer using Java Swing UI
Usage: java -jar dist/swingvcfview.jar [options] Files
Usage: swingvcfview [options] Files
Options:
--gff, --gff3
GFF3 file Path used to find intervals by gene name
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-r, --regions, --interval
default interval region on opening
Default: <empty string>
--limit
Limit number of variants. Ignore if < 0
Default: -1
--pedigree
A pedigree file. tab delimited. Columns: family,id,father,mother,
sex:(0:unknown;1|male|M:male;2|female|F:female), phenotype
(-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected)
--version
print version and exit
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew swingvcfview
The java jar file will be installed in the dist
directory.
20210503
The project is licensed under the MIT license.
Should you cite swingvcfview ? 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/swingvcfview.jar input.vcf.gz