VAGrENT

Variation Annotation GENeraTor

A suite of perl modules that compares genomic variations with reference genome annotations and generates the possible effects each variant may have on the transcripts it overlaps. It evaluates each variation/transcript combination and describes the effects in the mRNA, CDS and protein sequence contexts. It provides details of the sequence and position of the change within the transcript/protein as well as Sequence Ontology terms to classify its consequences.

Master	Dev

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Dependencies/Install

Some of the code included in this package has dependencies on several packages:

• Samtools v1.3+
• vcftools
• Bio::DB::HTS
• bedtools2
  • Not >=2.24.0, no upgrades until this ticket is resolved (which may involve code changes)

And various perl modules.

Please use setup.sh to install the dependencies. Setting the environment variable CGP_PERLLIBS allows you to to append to PERL5LIB during install. Without this all dependancies are installed into the target area.

Please be aware that this expects basic C compilation libraries and tools to be available.

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Creating a release

Preparation

• Commit/push all relevant changes.
• Pull a clean version of the repo and use this for the following steps.

Cutting the release

1. Update lib/Sanger/CGP/Vagrent.pm to the correct version.
2. Update CHANGES.md to show major items.
3. Run ./setup.sh /path/to/local/inst to create a local installation
4. Ensure your build enviroment contains Devel::Cover, Template and Pod::Coverage::CountParents. These can be loaded at the Sanger with module load perl-testlibs
5. Run ./prerelease.sh /path/to/local/inst
6. Check all tests and coverage reports are acceptable.
7. Commit the updated docs tree and updated module/version.
8. Push commits.
9. Use the GitHub tools to draft a release.

LICENCE

Copyright (c) 2014-2019 Genome Research Ltd.

Author: CASM/Cancer IT [email protected]

This file is part of VAGrENT.

VAGrENT is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.

1. The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- 2009, 2011-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012’."