Read Me

###### SVMerge ######
# kw10@sanger.ac.uk #
# tk2@sanger.ac.uk  #
# June 2011         #
# Version 1.1       #
#####################


SVMerge is a pipeline to call and computationally validate large structural variation (SV) calls
generated from several software, which use different analysis methods and algorithms to identify
candidate SVs. SVMerge can be used to set up a new SV calling project, run SV callers, merge
redundant calls, set up and run local assemblies, align resultant contigs, parse and interpret contig
alignments to validate SV calls and adjust breakpoints.

SVMerge is freely available for download at http://svmerge.sourceforge.net.

 - NOTE: THE COMPLETE DOCUMATATION IS PROVIDED IN THE SVMerge PACKAGE. -

Reference: Wong K, Keane TM, Stalker J, Adams DJ. Enhanced structural variant and breakpoint 
detection using SVMerge by integration of multiple detection methods and local assembly.

Genome Biol. 2010;11(12):R128. Epub 2010 Dec 31. http://genomebiology.com/content/11/12/R128

Important Notes:

- The pipeline scripts are written in Perl and bash. All SVMerge scripts must be maintained in the
same directory (eg: /home/user/src/svmerge/).

- Along with SVMerge and the additional software listed below, the only requirements are BAM files,
reference FASTA files, and a configuration file which specifies all parameters used in SVMerge. A
template configuration file is included in this package.

- Ideally, particular steps in the SVMerge pipeline should be run using a compute farm, especially
with large data sets. SVMerge provides scripts to submit jobs jobs using the Platform LSF cluster
management system (LSF). Commands to run specific steps without LSF are also provided.

- Any file with coordinates for SVs or any other genomic features should be in tab-delimited or BED
format (http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED). This is required
since BEDTools (see Additional Software section below) is used in the pipeline. Chromosomes
can be either {1, 2, ... , X, Y} or {chr1, chr2, ... , chrX, chrY}, however the same
naming convention must be used in all .tab or .bed files. These should also be consistent with
chromosome names in your BAM and reference FASTA files.



Additional software:


Additional software required for SVMerge are freely available. Currently, SVMerge supports SV
callers BreakDancerMax, Pindel, cnD and SECluster. These are available at:

https://trac.nbic.nl/pindel/downloads/ (Pindel\_source\_v0.2.3.zip)

http://sourceforge.net/projects/breakdancer/

http://www.sanger.ac.uk/resources/software/cnd/

SECluster is included in the SVMerge package.

http://sourceforge.net/projects/rdxplorer/ (No longer supported)

The BEDTools package is required for coordinate comparison:

http://code.google.com/p/bedtools/

The Samtools package is required to read and manipulate BAM files:

http://sourceforge.net/projects/samtools/

The aligner for the contig alignments in the local assembly validation step is Exonerate:

http://www.ebi.ac.uk/~guy/exonerate/

The pipeline scripts also use the Perl module Set::IntSpan, which can be downloaded from CPAN:

http://search.cpan.org/dist/Set-IntSpan/