cgpCaVEManPostProcessing

cgpCaVEManPostProcessing is used to apply filtering on raw VCF calls generated using CaVEMan.

For details of the underlying algorithm please see the CaVEMan site.

Master	Dev

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Dependencies/Install

Please install the following first:

• cgpVcf
• Bio::DB::HTS
  • If you have an install of PCAP-core this is already available

Please see these for any child dependencies.

setup.sh will install bedtools for you.

Once complete please run:

./setup.sh /some/install/location

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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 perl/lib/Sanger/CGP/CavemanPostProcessor.pm to the correct version.
2. Run ./prerelease.sh
3. Check all tests and coverage reports are acceptable.
4. Commit the updated docs tree and updated module/version.
5. Push commits.
6. Use the GitHub tools to draft a release.

LICENCE

Copyright (c) 2014-2017 Genome Research Ltd.

Author: Cancer Genome Project cgpit@sanger.ac.uk

This file is part of cgpCaVEManPostProcessing.

cgpCaVEManPostProcessing 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’."