jvarkit

SwingBamCov

Last commit

Bam coverage 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 swingbamcov  [options] Files

Usage: swingbamcov [options] Files
  Options:
    --bed
      Load this bed file and use the intervals as a set of menus to jump to a 
      specific location.
    --gtf, --gff
      GFF3 file indexed with tabix to plot the genes.
    -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>
    -q, --mapq
      min mapq
      Default: 1
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --small
      Display the reads when the region is small than 'x' bp. A distance 
      specified as a positive integer.Commas are removed. The following 
      suffixes are interpreted : b,bp,k,kb,m,mb,g,gb
      Default: 200
    --version
      print version and exit

Keywords

Creation Date

20210420

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfviewgui/SwingBamCov.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite swingbamcov ? 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/swingbamcov.jar -R ref.fa *.bam

Screenshot

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