VAGrENT README.TXT

INTRODUCTION

VAGrENT is a tool set for Variant Annotation Generator. It compares genomic variants 
against a reference genome annotation and attempts to identify the biological 
consequences those variants may cause.

VAGrENT consists of a group of perl modules and a handful of example scripts showing
how they can be used.

INSTALLATION

VAGrENT consists purely of perl code, so installation is simple a case of
unzipping and pathing to the modules.

SYSTEM REQUIREMENTS

Perl 5.8 or later.  Modules are generally tested in perl 5.8.8 and above.

DEPENDENCIES

The following packages are used by VAGrENT and will need to be installed before it
will function

Log::Log4perl -> used for the logging within VAGrENT (1.12 tested)
BioPerl -> used for some simple sequence manipulation (1.5.2 and 1.6.1 tested)

There are also some optional dependencies

Test::More -> required if you want to run the unit tests (recommended)
Ensembl core API -> required if you want to use Ensembl as your reference transcript
                    source.  The packaged adapter has been tested with API version 58
                    and higher.
										
										
PROJECT ORGANISATION

docs/     - documentation
testdata/ - reference test data for unit testing 
perl/     - all perl code

perl/config/  - configuration files
perl/modules/ - all perl modules 
perl/scripts/ - example perl scripts
perl/tests/   - unit test scripts