VcfToSvg

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 exits
  * -k, --knownGenes
      Tabix indexed UCSC knownGene file. Beware with the name of the 
      chromosomes: they should be the same than in your VCF
    -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 exits

##Description

write a vcf to svg , with gene context

##Keywords

• vcf
• svg
• xlm
• visualization

##Compilation

Requirements / Dependencies

• java compiler SDK 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
• GNU Make >= 3.81
• curl/wget
• git
• xsltproc http://xmlsoft.org/XSLT/xsltproc2.html (tested with "libxml 20706, libxslt 10126 and libexslt 815")

Download and Compile

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

The *.jar libraries are not included in the main jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). The required libraries will be downloaded and installed in the dist directory.

edit 'local.mk' (optional)

The a file local.mk can be created edited to override/add some definitions.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

Source code

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