jvarkit

VcfServer

Web Server displaying VCF file. A web interface for vcf2table

Usage

Usage: vcfserver [options] Files
  Options:
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -jexl, --jexl
      Use/Show JEXL filter instead of Javascript filter (which is not 
      filesystem-safe). 
      Default: false
    -p, --ped, --pedigree
      Optional Pedigree file:A pedigree is a text file delimited with tabs. No 
      header. Columns are (1) Family (2) Individual-ID (3) Father Id or '0' 
      (4) Mother Id or '0' (5) Sex : 1 male/2 female / 0 unknown (6) Status : 
      0 unaffected, 1 affected,-9 unknown
    -P, --port, -port
      Server listening port
      Default: 8080
    -timeout, --timeout
      query timeout in seconds
      Default: 60
    --url
      A custom URL for a web browser. The following words will be replaced by 
      their values: ${CHROM}, ${START}, ${END}. For example for IGV that would 
      be: 'http://localhost:60151/goto?locus=${CHROM}%3A${START}-${END}' (see 
      http://software.broadinstitute.org/software/igv/book/export/html/189) 
    --version
      print version and exit

Keywords

• vcf
• table
• visualization
• server
• web

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 vcfserver

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/vcfserver/VcfServer.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 vcfserver ? 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 VCF file (tabix or tribble) or a file containing the path to the VCFs.

Screenshot

https://twitter.com/yokofakun/status/923870331659485184

https://twitter.com/yokofakun/status/924307836968079361

Example

$ java -jar dist/vcfserver.jar input.vcf.gz

2017-10-27 23:53:04.140:INFO::main: Logging initialized @510ms
[INFO][VcfServer]Starting com.github.lindenb.jvarkit.tools.vcfserver.VcfServer on http://localhost:8080
2017-10-27 23:53:04.223:INFO:oejs.Server:main: jetty-9.3.7.v20160115
2017-10-27 23:53:04.336:INFO:oejs.ServerConnector:main: Started ServerConnector@9a8472{HTTP/1.1,[http/1.1]}{0.0.0.0:8080}
2017-10-27 23:53:04.337:INFO:oejs.Server:main: Started @717ms

This site is open source. Improve this page.