CoverageGrid

Display an image of depth to display any anomaly an intervals+bams as a grid image

Usage

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

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

Usage: coveragegrid [options] Files
  Options:
    --dimension, --dim
      Image Dimension. a dimension can be specified as '[integer]x[integer]' 
      or the word 'screen' or it can be the path to an existing 
      png,jpg,xcf,svg file.
      Default: java.awt.Dimension[width=1000,height=300]
    --extend, -x
      extends the interval x times
      Default: 3.0
    --format
      output format
      Default: SVG
      Possible Values: [SVG, SVG_GZ, PNG, JPG, PS, PS_GZ, TXT]
    --gtf
      indexed GTF file to show genes
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * --regions, --region, --interval
      Interval region
    --inversion-flag
      for DISCORDANT or SUPPL : arcs as a edge outside interval and the other 
      inside the interval
      Default: false
    --known
      Known CNV: can be an indexed vcf.gz file or a tabix bed.gz file.
    --mapq
      min mapping quality
      Default: 1
    --max-y
      Max normalized Y, when using --type MEDIAN_COVERAGE
      Default: 3.0
    -o, --output
      Output file. Optional . Default: stdout
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    --threads
      number of threads
      Default: 1
    --title
      Set Title for graphics
      Default: <empty string>
    --type, --what, --plot
      Plot type. COVERAGE: DEPTH of coverage, MEDIAN_COVERAGE: coverage 
      normalize by external boundaries, PILEUP: show reads, PILEUP_PAIR: show 
      paired-end fragments, GRID: matrix of read name co-occurence. Slow and 
      memory consuming.,DISCORDANT: plot discordant reads as arcs overlaping 
      edges, SUPPL: plot sipplementary read pairs as arcs overlaping edges
      Default: MEDIAN_COVERAGE
      Possible Values: [COVERAGE, MEDIAN_COVERAGE, PILEUP, PILEUP_PAIR, GRID, DISCORDANT, SUPPL]
    --vcf
      indexed VCF file to show variants
    --version
      print version and exit
    -D
      other parameters '-Dkey=value'. -Dhide_insertions=true 
      -Dinversion_mode=true -Doverlap_boundaries=true
      Syntax: -Dkey=value
      Default: {}

Keywords

• cnv
• bam
• depth
• coverage
• svg
• postscript

Creation Date

20241009

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/coveragegrid/CoverageGrid.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 coveragegrid ? 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

input

input is a tab-delimited samplesheet with the following columns:

column	required ?	description
bam	required	/path/to/indexed/bam+or+cram
color	optional	color used for frame (could be a hint to spot cases/controls). Can be empty. Otherwise, use default color
sample	optional	sample name. If empty the sample will be extracted from the bam. If it starts with '+=' , the name will appended to the original bam name

example:

find dir -type f -name "*bam" > in.list 
java -jar dist/jvarkit.jar coveragegrid -R src/test/resources/rotavirus_rf.fa --region "RF01:100-200" in.list