hammerlab/igvxml

Name: igvxml

Owner: Hammer Lab

Description: Create IGV session files from the command-line

Created: 2016-07-22 15:45:04.0

Updated: 2017-02-13 23:29:44.0

Pushed: 2017-02-14 18:14:01.0

Homepage: null

Size: 13

Language: OCaml

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README

Generate IGV Session Files from the Command Line

Install the library and the binary with opam install igvxml.

To build from source:

 deps  # If you don't have them yet
       # sosa nonstd cmdliner xmlm
       # Results in a ./igvxml binary.

You can use it like so:

ml --help


   igvxml - Create an IGV session file.

PSIS
   igvxml [OPTION]...

ONS
   -G VAL, --genome=VAL
       Genome used. b37decoy or mm10.

   --help[=FMT] (default=pager)
       Show this help in format FMT (pager, plain or groff).

   -N VAL, --normal-bam=VAL
       Path to Normal BAM.

   -O VAL, --output=VAL
       XML session file to be written.

   -R VAL, --rna-bam=VAL
       Path to RNA BAM. (optional)

   --run-id=VAL
       Patient/Run ID.

   -T VAL, --tumor-bam=VAL
       Path to Tumor BAM.

   -V VAL, --vcfs=VAL
       List (comma-separated) of name=path VCFs.

   --version
       Show version information.

ription
   Create an IGV.xml session file from the specified arguments.

igvxml is built for somatic paired BAMs and multiple VCFs, with optional RNA seq data.

Contributions welcome for making this more general.