Web Server displaying VCF file. A web interface for vcf2table
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
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfserver
The java jar file will be installed in the dist
directory.
The project is licensed under the MIT license.
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 is a set of indexed VCF file (tabix or tribble) or a file containing the path to the VCFs.
https://twitter.com/yokofakun/status/923870331659485184
https://twitter.com/yokofakun/status/924307836968079361
$ 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