msvtools explores microarray data for genomic structural variants, specifically CNVs. msvtools implements the analysis logic of VAMP as described here:
Arlt MF, Ozdemir AC, Birkeland SR, Lyons RH Jr, Glover TW, Wilson TE. Comparison of constitutional and replication stress-induced genome structural variation by SNP array and mate-pair sequencing. Genetics. 2011 187:675-83.
msvtools is a suite of scripts that manage data flow through a series of open-source third-party programs and applications.
Command line tools run under a Linux or compatible environment.
System prerequisites for running msvtools in the analysis phase are:
Perl: http://www.perl.org/
R: http://www.r-project.org/ (plus package mixtools for the train command)
in addition to other standard Linux system utilities. The installation utility will apprise you if you are missing a prerequisite. Note that msvtools cannot be run on Windows in the analysis phase.
Folder 'msvtools/q-scripts' carries q master scripts for running msvtools analysis using the q-pipeline-manager.
System prerequisites for running msvtools in the visualization phase are:
Perl: http://www.perl.org/
in addition to specific perl packages listed in INSTALL.
Read the INSTALL file to learn how to use the 'configure.pl' installation script.
msvtools encompasses a series of commands called as follows:
msvtools <command> [options]Use:
msvtools -h/--help
msvtools <command> -h/--helpfor more information on individual commands and their options.
At present, msvtools is only well tested on Illumina Bead Array data. It is expected that you have folder(s) with the standard folder structure ultimately containing FinalReport files for the run(s) and DNAReport files for the samples.