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:
- Collect read-pairs where both ends map but NOT marked as properly-paired.
- Perform grouping based on mapped locations
- Filter
- Run assembly
- Annotate with GRASS
./setup.sh path_to_install_to
- The C++ code (within this package) requires the presence of pstreams.h (and associated development libraries). This is not handled by the
setup.shscript.
A large number of R packages are required to run BRASS. To facilitate the install process there is a script Rsupport/libInstall.R that can be run to build these for you. See this file for the list of packages.
Alternatively you can run:
cd Rsupport
./setupR.sh path_to_install_to
Appending 1 to the command will request a complete local build of R (3.1.3).
- FASTA
- If not done failures due to absence of
ssearch36will occur. ssearch36is the only program required.
- If not done failures due to absence of
Please use setup.sh to install these 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. setup.sh will not use PERL5LIB directly.
Please be aware that this expects basic C compilation libraries and tools to be available.
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:
- 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
- Farm style
- Requires 2 extra parameters in the initial command
- See
-helpfor further details
BRASS has primarily been written to work with BWA mapped data. You are likely to get the most useful output from BWA-mem.
Please be aware that paired-end libraries where properly-paired reads overlap are unlikely to produce good results.
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.
Copyright (c) 2014-2016 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/.
- 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’."