August 8 2010
SNPPicker is a post-processor to optimize the selection of tag SNPs from 
common bin-tagging programs. SNPPicker uses a multi-step search strategy 
in combination with a statistical model to produce optimal genotyping panels. 
SNPPicker’s algorithm is also designed to optimize tag SNP selection for 
multi-population panels. It accounts for several assay-specific constraints 
such as predicted assay failure of SNPs and avoidance of SNPs that are too close.  The latter issue affects one third of all SNPs in the 1000 genomes project pilot 1 data.
SNPPicker automates the design of tag SNP genotyping panels by maximizing 
the likelihood of successfully genotyping the selected SNPs while minimizing 
the number of tag SNPs to assay. Geno-typing success is a function of two 
properties:  the genotyping probability of a bin (or cluster of bins) 
statistically derived from the individual genotyping probability of each SNP; 
and (for some platforms) the proximity distance between SNPs. 
The genotyping probabilities currently used by SNPPicker are derived a from 
pro-spective analysis of the performance of genotyping assay and the probability 
model can be updated or changed for other platforms. SNP proximity is a strictly
enforced constraint
 
 
The SNPPicker manuscript is currently under review for Bioinformatics
submitted aug 2010 
SNPPicker: High quality tag SNP selection across multiple populations.
Hugues Sicotte, David N. Rider, Gregory A. Poland , Neelam Dhiman , Jean-Pierre A. Kocher


This is SNPPicker version 2, the version described in the paper.
It involved a significant rewrite of SNPPicker 1, yet yields similar results.
However, this SNPPicker 2 has been extensively tested and always returns a solution.


SNPPicker requires at least java 1.5

A user manual is under preparation, but command and basic options can be listed using

java -jar SNPPicker.jar -h

RunSNPPicker2.pl: a perl program to automates the running of SNPPicker when building a multi-gene panel. 
Each population must be under it's own directory structure.
Details will be in the user manual.

TagSolutionReport.pl: a perl program to parse the output of SNPPicker or RunSNPPicker2.pl 
and produces a summary report.

A file Commands_example2.txt lists some of the commands used in this paper. 
They will not work as the parameter files are not supplied.