jvarkit

VcfToSvg

write a vcf to svg , with gene context

Usage

Usage: vcf2svg [options] Files
  Options:
    --alphaFILTER
      Variant having FILTER!=PASS opacity (0== hide FILTERED variants)
      Default: 1.0
    --alphaINDEL
      Variant INDEL opacity (0== hide INDEL variants)
      Default: 1.0
    --exon, --exons
      Only keep variants in exons
      Default: false
    -gw, --genotypeWidth
      Genotype square width
      Default: 10
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
  * -k, --knownGenes
      UCSC knownGene File/URL. The knowGene format is a compact alternative to 
      GFF/GTF because one transcript is described using only one line.	Beware 
      chromosome names are formatted the same as your REFERENCE. A typical 
      KnownGene file is 
      http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz 
      .If you only have a gff file, you can try to generate a knownGene file 
      with [http://lindenb.github.io/jvarkit/Gff2KnownGene.html](http://lindenb.github.io/jvarkit/Gff2KnownGene.html)
    -m, --manifest
      Manifest file containing the names of the files.
    --nonCoding
      Ignore Non-coding genes
      Default: false
    -o, --out
      Output SVG file. If defined, MUST Contains the word '__SEGMENT__'
    --stopAfterFirst
      when writing multiple SVG docs, stop after the first one. It avoids 
      writing multiple concatenated SVG documents when writing to stdout
      Default: false
    -trim2ctx, --trimToVariant
      Don't use gene interval for graphics but min/max of variants
      Default: false
    --version
      print version and exit

Keywords

• vcf
• svg
• xlm
• visualization

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcf2svg

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfToSvg.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/VcfToSvgTest.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 vcf2svg ? 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

# download and gzip refGene from UCSC
$ curl -s "http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz" |\
   gunzip -c | LC_ALL=C sort -t '	' -k3,3 -k5,5n | bgzip > refGene.txt.gz

# index the refGene file
$ tabix  -0 -s  3 -b 5 -e 6 -f refGene.txt.gz

# run vcf2svg 
$ java -jar dist/vcf2svg.jar \
   --stopAfterFirst \
   -k refGene.txt.gz input.vcf > out.svg

Screenshot

https://twitter.com/yokofakun/status/851875435948462080

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