visualization for variants and attributes using https://visdunneright.github.io/sequence_braiding/docs/ .
Usage: vcfbraiding [options] Files
Options:
--alleles
show alleles in header.
Default: false
-B, --base
Base URL for code
:https://visdunneright.github.io/sequence_braiding/docs/
Default: https://visdunneright.github.io/sequence_braiding/docs/
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--hom-ref, -hr
remove sample that are all HOM_REF for all variants.
Default: false
--id
id for svg element.
Default: vcfid
--no-call, -nc
remove sample that are all NO_CALL for all variants.
Default: false
-o, --output
Output file. Optional . Default: stdout
-T, --title
title
Default: <empty string>
--version
print version and exit
-D
Dynamic parameters for API 'options'. -Dkey=value . Keys are currently:
show_seq_names forceLevelName animate colorbysequence width height
fontSize padding.
Syntax: -Dkey=value
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 vcfbraiding
The java jar file will be installed in the dist
directory.
20201021
The project is licensed under the MIT license.
Should you cite vcfbraiding ? 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
bcftools view src/test/resources/rotavirus_rf.vcf.gz "RF02" "RF03" |\
java -jar /home/lindenb/src/jvarkit-git/dist/vcfbraiding.jar --title "Rotavirus Variants" > variants.html
https://twitter.com/yokofakun/status/1319221221611941889
https://twitter.com/yokofakun/status/1319228442043387905
## See also: