ScatterShot Version 0.74 beta

Requirements: Java 7
Java 7 is available from Oracle here: http://www.oracle.com/technetwork/java/javase/downloads/index.html
For Unix/Linix there may be an OpenJDK implementation available with your OS.

Usage
Once unzipped we provide script files in the bin directory. These scripts require
a properties file, which provide arguments for the program (rather than specifying
on the command line).

These can be called 
from the command console.
Unix: sh bin/scattershot.sh PATH_TO_PROPERTIES
Windows: bin/scattershot.bat PATH_TO_PROPERTIES

Example data and properties files can be found in the examples directory. 
To test your installation run example data. Change to the examples directory. 
Run: sh ../bin/scattershot.sh example1.var1.properties
This will create a directory example1.var1.clusters/ with example clusterplots.

The "task_id" property tells ScatterShot which task to execute. Current tasks are:

ClusterPlot 
        For turning xy component files to cluster plots, both Affy and Illumina
        scales supported. Example 1 is a test set using Illumina-scale data,
        whereas example 2 uses the Affy-scale.

IlluminaFinalReportTransform 
        For turning IlluminaFinalReports into component matrices. See example 3
        for more instruction.

AffyChpExtract 
        For extracting xy and allele data from Affymetrix binary chp files.
        See example 4 properties file for required parameters, etc. Unfortunately
        we do not have any available .chp files for distribution. 

Transpose 
        For flipping the axes of character-separated tables. See example 5 for 
        more instruction.

The files from example 3 (parts 1 and 2) show how to convert a FinalReport and 
plot clusters for a subset of markers.

The "xy_stem" property points the program to the xy matrix files to be used. 
When the Final Report exact is run, 6 component files are created.

example3.marker.gz The list of marker ids in the component files. In a typical 
        sample major extract these are the columns.
example3.indiv.gz The list of individuals in the component files. In a typical
        samples major extract these are the rows.
example3.xy.gz The tab-separated normalized XY data. 
example3.allele.gz The tab-separated allele data.
example3.logr.gz The tab-separated logr and ballele fields.
example3.raw_xy.gz The tab-separated raw XY data, not normalized.

If you are plotting from a BED file then only xy, marker and indiv files are required.

The mandatory "xy_snp_inclusion" property points to a file with a list of marker ids. This 
        informs the program which markers need to be included.

The "xy_ind_inclusion" property tells the program which individuals need to be included.

The "allele_stem" property points to a series of BED, BIM, FAM files from which 
        individual, marker and allele information is to be loaded.

The "IOProperties.OUT_DIRECTORY" property is the directory into which resulting PNG 
files will be placed.

All input files (including final report) may be gzipped. If so ensure they have
the .gz suffix.

NRR 2013DEC09
