SeqWare/seqware-sandbox — pull request #6 by bcso (2014-01-23 20:37:13+00:00)
Title: Feature/gatkimplement

The main function is GATKBackendTest. Please follow the instructions below to setup the testing process.

NOTE:
Feel free to use the included input VCF and JSONQuery (.txt) input included in the resources folder (for step 3). These have been tested against the main function and have worked.

1. Please download the package dependancies required to compile:

git clone https://github.com/bcso/gatk.git

2. Add all packages to build path of project.

3. In the main method, you may point to a:
INPUT:
* local VCF file
* local JSONfile (in a text format)

OUTPUT:
* a TSV output

4. Compile!