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cgpVAF

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vafCorrect

Calculates the Variant Allele Fraction for variants sites in VCF and/or BED file This script performs comparative analysis of variant sites in multiple tumour/normal samples in an individual. Also facilitates the merging of varinats sites across the samples in a sample group defined by set of related samples in an individual and provides unbiased pileup[MNV] and exonerate[Indel] output for each variant site.

Quick installation

./setup.sh path_to_install_to

Skipping all external dependencies

If you want to only install vafCorrect and use existing versions of tools from your path run as:

./setup.sh path_to_install_to 1

vcftools and htslib still need to install in this instances as they have perl module bindings which are required dependencies.

Skipping exonerate install

Central install via package manager of 2.2.0 is adequate. To skip just exonerate install run:

./setup.sh path_to_install_to 2

INSTALL

Dependencies

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

setup.sh should install these dependencies.

./setup.sh /some/install/location

Please be aware that this expects basic C compilation libraries and tools to be available, most are listed in INSTALL.

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/Vaf.pm and the label in Dockerfile to the correct version.
  2. Update CHANGES.md to show major items.
  3. Run ./perl/prerelease.sh
  4. Check all tests and coverage reports are acceptable.
  5. Commit the updated docs tree and updated module/version.
  6. Push commits.
  7. Use the GitHub tools to draft a release.

LICENCE

Copyright (c) 2017-2020 Genome Research Ltd.

Author: CASM/Cancer IT <[email protected]>

This file is part of vafCorrect.

vafCorrect 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’."