SwingBamCov
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
- bam
- alignment
- graphics
- visualization
- swing
Creation Date
20210420
Source code
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 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
- https://twitter.com/yokofakun/status/1392173415684100105
- https://twitter.com/yokofakun/status/1443187891480502279
- https://twitter.com/yokofakun/status/1443208754229563392