jvarkit

BamToSVG

BAM to Scalar Vector Graphics (SVG)

Usage

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

Usage: java -jar dist/jvarkit.jar bam2svg  [options] Files

Usage: bam2svg [options] Files
  Options:
    --bases
      print bases in read
      Default: false
    --gff, --gff3
      Optional Tabix indexed GFF3 file.
    --groupby
      Group Reads by. 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]
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -i, --interval, --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)
    --mapq
      min mapping quality
      Default: 1
  * -o, --output
      An existing directory or a filename ending with the '.zip' or '.tar' or 
      '.tar.gz' suffix.
    --prefix
      file prefix
      Default: <empty string>
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard/gatk CreateSequenceDictionary or samtools dict
    -c, --showclipping, --clip
      Show clipping
      Default: false
    -S, --vcf
      Indexed VCF. the Samples's name must be the same than in the BAM
    --version
      print version and exit
    -w, --width
      Page width
      Default: 1000
    -D
      custom parameters. '-Dkey=value'. Undocumented.
      Syntax: -Dkey=value
      Default: {}

Keywords

• bam
• alignment
• graphics
• visualization
• svg

Creation Date

20141013

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bam2svg/BamToSVG.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/bam2svg/BamToSVGTest.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 bam2svg ? 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 set of indexed BAM/CRAM files or a file with the path to the bam with the ‘.list’ suffix.

Example

$ find dir dir2 -type f -name "*.bam" > file.list

$ java -jar dist/bam2svg.jar \
    -R human_g1k_v37.fasta \
    -i "19:252-260" \
    -S variants.vcf.gz \
    -o output.zip
    file.list

Gallery

https://twitter.com/yokofakun/status/523031098541232128

https://twitter.com/yokofakun/status/522415314425090048

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