jvarkit

SvToSVG

Last commit

BAM to SVG. Used to display structural variations.

Usage

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

Usage: java -jar dist/jvarkit.jar sv2svg  [options] Files

Usage: sv2svg [options] Files
  Options:
    --coverage, --depth
      Coverage height. Don't print if cov '<=0'.
      Default: 70
    -d, --duration
      Animation duration, in secs. <=0 disable animation.
      Default: 10
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -r, -i, --interval, --region
      interval CHROM:START-END
      Default: []
    --mapq, --Q
      min mapping quality
      Default: 1
    --mismatch
      do not display bases mismatches between read and REF.
      Default: false
    -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
    --repeat-count
      SVG animation repeat count
      Default: indefinite
    --strange
      Keep only non-properly-paired , soft clipped and SA:X:* reads.
      Default: false
    --svg
      Write SVG only document. Default is to write a XHTML+SVG document.
      Default: false
    --variant, -V
      optional indexed VCF file.
    --version
      print version and exit
    -w, --width
      Page width
      Default: 1000

Keywords

bam
alignment
graphics
visualization
svg
structural
variant

Creation Date

20181115

Source code

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

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/bam2svg/SvToSVGTest.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 sv2svg ? 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

$ samtools view -b "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA20845/high_coverage_alignment/NA20845.wgs.ILLUMINA.bwa.GIH.high_cov_pcr_free.20140203.bam" "7:8352157-8356597" > jeter.bam && samtools index jeter.bam
$ java -jar dist/jvarkit.jar svg2svg jeter.bam > jeter.html

A translocation

Translocation described in PMC5932280

Identification of Balanced Chromosomal Rearrangements Previously Unknown Among Participants in the 1000 Genomes Project: Implications for Interpretation of Structural Variation in Genomes and the Future of Clinical Cytogenetics

$ samtools view -b "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG02260/alignment/HG02260.mapped.ILLUMINA.bwa.PEL.low_coverage.20130415.bam" "9:137229907-137231907" > jeter1.bam
$ samtools view -b "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG02260/alignment/HG02260.mapped.ILLUMINA.bwa.PEL.low_coverage.20130415.bam" "14:79838174-79840174" > jeter2.bam
$ samtools merge jeter3.bam jeter1.bam jeter2.bam
$ samtools index jeter3.bam
$ java -jar dist/jvarkit.jar sv2svg -r "9:137229907-137231907" -r "14:79838174-79840174"  jeter3.bam > jeter.html