jvarkit

SwingBamView

Read viewer using Java Swing UI

Usage

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

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

Usage: swingbamview [options] Files
  Options:
    --gff, --gff3
      Tabix-Indexed GFF3 File
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    -V, --variant
      Indexed VCF File
    --version
      print version and exit

Keywords

• bam
• alignment
• graphics
• visualization
• swing

Creation Date

20220503

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfviewgui/SwingBamView.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 swingbamview ? 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 swingbamview -R src/test/resources/rotavirus_rf.fa src/test/resources/S*.bam

find dir -type f -name "*.bam" > out.list
java -jar dist/jvarkit.jar swingbamview -R src/test/resources/rotavirus_rf.fa out.list

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