LICENCE

Copyright (c) 2014,2015 Genome Research Ltd.

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

This file is part of BRASS.

BRASS 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’."

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BRASS

BReakpoint AnalySiS

BRASS analyses one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints.

There are several stages the main component being:

1. Collect read-pairs where both ends map but NOT marked as properly-paired.
2. Perform grouping based on mapped locations
3. Filter
4. Run assembly
5. Annotate with GRASS

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Installation

./setup.sh path_to_install_to

Pre-requisites

• The C++ code requires the presence of pstreams.h (and associated development libraries). This is not handled by the setup.sh script.
• PCAP-core
• cgpVcf

Running BRASS

This package includes a reference implementation which handles all of the linking together of steps.

Please see the -h and -m options of brass.pl for full usage information.

It can be run in a couple of ways:

1. Fire and forget

• Execute on a single host with multiple cores (or 1 if that's all you have)
• Some efficiency overhead as some steps aren't parallel

2. Farm style

• Requires 2 extra parameters in the initial command
• See -help for further details

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Input

Initial mapping

BRASS has primarily been written to work with BWA mapped data. You are likely to get the most useful output from BWA-mem.

Library quality

Please be aware that paired-end libraries where properly-paired reads overlap are unlikely to produce good results.

Additional mapping information

BRASS requires accurate information regarding the insert size distribution and expects to find a *.bam.bas file co-located with the *.bam's. These can be generated by the bam_stats program included in the PCAP-core project. If you use bwa_mem.pl to map your data (same repository) then this file is generated automatically for you.