WGSCoveragePlotter
Whole genome coverage plotter
Usage
This program is now part of the main jvarkit
tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar wgscoverageplotter [options] Files
Usage: wgscoverageplotter [options] Files
Options:
--clip, --cap
Don't show coverage to be greater than 'max-depth' in the SVG file.
Default: false
--dimension
Image Dimension. a dimension can be specified as '[integer]x[integer]'
or it can be the path to an existing png,jpg,xcf,svg file.
Default: java.awt.Dimension[width=1000,height=500]
--disable-paired-overlap
Count overlapping bases with mate for paired-end
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-I, --include-contig-regex
Only keep chromosomes matching this regular expression. Ignore if blank.
Default: <empty string>
--mapq
min mapping quality
Default: 1
-C, --max-depth
Max depth to display. The special value '-1' will first compute the
average depth and the set the max depth to 2*average
Default: 100
--min-contig-length
Skip chromosome with length < 'x'. A distance specified as a positive
integer.Commas are removed. The following suffixes are interpreted :
b,bp,k,kb,m,mb,g,gb
Default: 0
-o, --output
Output file. Optional . Default: stdout
--partition
When using the option --samples, use this partition Data partitioning
using the SAM Read Group (see
https://gatkforums.broadinstitute.org/gatk/discussion/6472/ ) . It can
be any combination of sample, library....
Default: sample
Possible Values: [readgroup, sample, library, platform, center, sample_by_platform, sample_by_center, sample_by_platform_by_center, any]
--percentile
How to we bin the coverage under one pixel.
Default: median
Possible Values: [median, average, min, max]
--points
Plot the coverage using points instead of areas.
Default: false
* -R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard/gatk CreateSequenceDictionary or samtools dict
--samples
Limit to those groups. See also --partition. Multiple separated with
commas.
Default: <empty string>
-X, --skip-contig-regex
Skip chromosomes matching this regular expression. Ignore if blank.
Default: <empty string>
--version
print version and exit
-D
set some css style elements. '-Dkey=value'. Undocumented.
Syntax: -Dkey=value
Default: {}
Keywords
- svg
- bam
- depth
- coverage
See also in Biostars
- https://www.biostars.org/p/104063
- https://www.biostars.org/p/475162
- https://www.biostars.org/p/9536274
Creation Date
20201125
Source code
Unit Tests
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 wgscoverageplotter ? 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
Files
Input is an indexed BAM or CRAM file
Output is a SVG file
Example
java -jar dist/jvarkit.jar wgscoverageplotter --dimension 1500x500 -C -1 --clip -R src/test/resources/rotavirus_rf.fa src/test/resources/S1.bam --include-contig-regex "RF.*" --percentile median > ~/jeter.svg
Cited in
- Vinicius A.C & al. Comparative analyses of Theobroma cacao and T. grandiflorum mitogenomes reveal conserved gene content embedded within complex and plastic structures". Gene Volume 849 2023 .https://doi.org/10.1016/j.gene.2022.146904.
- Varani AM, Silva SR, Lopes S, Barbosa JBF, Oliveira D, Correa MA, Moraes AP, Miranda VFO, Prosdocimi F. 2022. The complete organellar genomes of the entheogenic plant Psychotria viridis (Rubiaceae), a main component of the ayahuasca brew. PeerJ 10:e14114 https://doi.org/10.7717/peerj.14114
- Cho, C.H., Park, S.I., Huang, TY. et al. Genome-wide signatures of adaptation to extreme environments in red algae. Nat Commun 14, 10 (2023). https://doi.org/10.1038/s41467-022-35566-x
- Rhys T. White, Martina Jelocnik, Natalie Klukowski, Md. Hakimul Haque, Subir Sarker. The first genomic insight into Chlamydia psittaci sequence type (ST)24 from a healthy captive psittacine host in Australia demonstrates evolutionary proximity with strains from psittacine, human, and equine hosts. Veterinary Microbiology, Volume 280, 2023, 109704, ISSN 0378-1135. https://doi.org/10.1016/j.vetmic.2023.109704.
- Rhys T. White. A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia's Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris). https://doi.org/10.1099/mgen.0.001101 . Microbial Genomics Vol9 Issue 9
- genomic and transcriptomic insight into the evolution and breeding of turfgrass species, poa annua and bouteloua dactyloides. Thesis. Christopher W. Benson. https://etda.libraries.psu.edu/files/final_submissions/29057 WGSCoveragePlotter
Screenshot
https://twitter.com/yokofakun/status/1331898068002861056