jvarkit

HtsFileServer

Last commit

Jetty Based http server serving Vcf and Bam files.

Usage

Usage: htsfileserver [options] Files
  Options:
    --gtf
      Optional GTF file. Will be used to retrieve an interval by gene name
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -G, --no-genotype
      remove genotypes from vcf
      Default: false
    --port
      server port.
      Default: 8080
  * -R, --reference
      Indexed fasta Reference file. This file must be indexed with samtools 
      faidx and with picard CreateSequenceDictionary
    --version
      print version and exit

Keywords

vcf
bam
server

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 htsfileserver

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

Creation Date

20200405

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/server/HtsFileServer.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 htsfileserver ? 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/Bam file or a file with the suffix .list containing the path to the files.

Example

java -jar dist/htsfileserver.jar -R src/test/resources/rotavirus_rf.fa src/test/resources/S*.bam  src/test/resources/rotavirus_rf.*.vcf.gz

Screenshot

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