cgpBattenberg

An installation helper, perl wrapper and the R program Battenberg which detects subclonality and copy number in matched NGS data.

Master	Dev

Installation

The battenberg R files are installed automatically from the Battenberg GitHub repository found here. The linked version is currently v2.2.5.

Please install the following before attempting to run setup.sh <install_to_folder> [X/lib/perl:Y/lib/perl]

1. PCAP-core v2.1.3+
2. alleleCount v3.0.1+
3. cgpVcf v2.0.1+

All of the items listed here use the same install method.

Prerequisites

• Impute2 executables can be found here
  • Any impute related data for download
• BWA Mapped, indexed, duplicate marked/removed bam files, for both a matched normal and tumour sample
• Reference.fasta and index
• A file containing a list of contigs in the reference .fai to ignore

Some required data files are not inclued in the distribution but a script is included to generate these for you:

• Directory containing the 1000 genomes allele and loci data:
  • Generated using the included script download_generate_bberg_ref_files.pl
• Impute info file impute_info.txt
  • Generated using the included script download_generate_bberg_ref_files.pl
• Prob loci file probloci.txt
  • Included: files/probloci.txt.gz

Program Run Instructions

For the most up to date usage instructions for the wrapper code please see the command line help:

battenberg.pl -h

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LICENCE

Copyright (c) 2014-2017 Genome Research Ltd.

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

This file is part of cgpBattenberg.

cgpBattenberg 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'."