jvarkit

BamMatrix

Bam matrix, inspired from 10x/loupe

Usage

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

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

Usage: bammatrix [options] Files
  Options:
    --color-scale
      Color scale
      Default: LOG
      Possible Values: [LINEAR, LOG]
    -d, --distance
      Don't evaluate a point if the distance between the regions is lower than 
      'd'. Negative: don't consider distance.
      Default: -1
    --gtf, -g
      Optional gtf file to draw the exons. A GTF (General Transfer Format) 
      file. See https://www.ensembl.org/info/website/upload/gff.html . Please 
      note that CDS are only detected if a start and stop codons are defined.
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --higligth, -B
      Optional Bed file to hightlight regions of interest
    --mapq
      minimal mapping quality
      Default: 30
    -C, --min-common
      Don't print a point if there are less than 'c' common names at the 
      intersection 
      Default: 0
    --name, -name
      user read name or use 'BX:Z:'/'MI:i:' attribute from 10x genomics  as 
      the read name. "Chromium barcode sequence that is error-corrected and 
      confirmed against a list of known-good barcode sequences.". See https://support.10xgenomics.com/genome-exome/software/pipelines/latest/output/bam
      Default: READ_NAME
      Possible Values: [READ_NAME, BX, MI]
    --no-coverage
      Don't print coverage
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    --pixel
      pixel size. Each dot at intersection will have the following size
      Default: 1
    -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
  * -r, -r1, --region
      first region.An interval as the following syntax : "chrom:start-end" or 
      "chrom:middle+extend"  or "chrom:start-end+extend" or 
      "chrom:start-end+extend-percent%".A program might use a Reference 
      sequence to fix the chromosome name (e.g: 1->chr1)
    -r2, --region2
      2nd region. Default: use first region. An interval as the following 
      syntax : "chrom:start-end" or "chrom:middle+extend"  or 
      "chrom:start-end+extend" or "chrom:start-end+extend-percent%".A program 
      might use a Reference sequence to fix the chromosome name (e.g: 1->chr1)
    -sa, --sa
      Use other canonical alignements from the 'SA:Z:*' attribute
      Default: false
    -s, --size
      matrix size in pixel
      Default: 1000
    -su, --supplementary
      Use other supplementary alignements
      Default: false
    --version
      print version and exit

Keywords

• sam
• bam
• compare
• matrix

Creation Date

20190620

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/cmpbams/BamMatrix.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/cmpbams/BamMatrixTest.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 bammatrix ? 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/bammatrix.jar -o out.png \
	--kg "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" \
	-r "chr1:2345-6789" -B cnv.bed --name BX \
	NOVASEQ/Sample/outs/phased_possorted_bam.bam

input with two bam files (for comparing mappers)

java  -jar dist/bammatrix.jar -r "chr1:234-567" -o out.png sample.markdup.01.bam sample.markdup.02.bam

https://twitter.com/yokofakun/status/1142088565326843904

https://twitter.com/yokofakun/status/1038060108373286912

This site is open source. Improve this page.