ReferenceToHtml

Produce a html view of eah interval from a VCF file

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar ref2html  [options] Files

Usage: ref2html [options] Files
  Options:
    ---prefix
      file prefix.
      Default: <empty string>
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -r, --region, --regions, --interval
      A source of intervals. The following suffixes are recognized: vcf, 
      vcf.gz bed, bed.gz, gtf, gff, gff.gz, gtf.gz.Otherwise it could be an 
      empty string (no interval) or a list of plain interval separated by '[ 
      \t\n;,]' 
  * -o, --output
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --version
      print version and exit

Keywords

• vcf
• html

Creation Date

20211012

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/ref2html/ReferenceToHtml.java

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 ref2html ? 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

Example

$ java -jar dist/jvarkit.jar ref2html -o TMP --regions "RF02:1-500" -R src/test/resources/rotavirus_rf.fa src/test/resources/rotavirus_rf.vcf.gz