This program is an implementation in C++ of the method for correcting the winner's curse in genetic association studies published in Genetic Epidemeology (2009):
http://www3.interscience.wiley.com/cgi-bin/fulltext/121591995/PDFSTART

The winner.exe file can be run in Unix platform directly. The command line will be:
./winner -input input_file_name -alpha > output_file_name

Here the input_file_name is the name of your input file; the alpha is the desired significance level; the output_file_name is the file name you'd like the results to be put in.

The input file will have 5 columns:
	column 1: SNP name
column 2: sample size for controls
column 3: sample size for cases
column 4: number of risk alleles in controls
column 4: number of risk alleles in cases

An example of the input file "sample_input.txt":

	SNP N0  N1  m0  m1
	rs1 100 200 50  150
	rs2 120 220 50  120
	rs3 200 180 100 120
	rs4 200 200 200 240

The header line is required for the input file. 

The sample output file "sample_output.txt":

	The significance level = 0.05
	The number of SNPs = 4
	SNP 	 N0 	 N1 	 m0 	 m1 	 naive_p 	 naive_d 	 naive_OR 	 as_mle_p 	 as_mle_d 	 as_mle_OR 	 asy_sd_p 	 asy_sd_d 	 asy_sad_OR 	 
	rs1 	 100 	 200 	 50 	 150 	 0.2500 	 0.1250 	 1.8000 	 0.2501 	 0.1248 	 1.7981 	 0.0351 	 0.0475 	 0.4228 	 
	rs2 	 120 	 220 	 50 	 120 	 0.2083 	 0.0644 	 1.4250 	 0.2085 	 0.0643 	 1.4244 	 0.0377 	 0.0559 	 0.4510 	 
	rs3 	 200 	 180 	 100 	 120 	 0.2500 	 0.0833 	 1.5000 	 0.2692 	 0.0415 	 1.2239 	 0.0327 	 0.0604 	 0.3596 	 
	rs4 	 200 	 200 	 200 	 240 	 0.5000 	 0.1000 	 1.5000 	 0.4999 	 0.1003 	 1.5016 	 0.0289 	 0.0451 	 0.2768 	 

The first line tells you what significance level you have chosen;
the second line is the number of SNPs in the file;
the third line is the header for the results.

From the fourth line, there are 14 columns:
column 1-5 is the same as the input file;
column 6-8 is the naive estimator for allele frequency, allele frequency difference between cases and controls, and OR, respetively;
column 9-11 is the ascertainment-corrected mle for allele frequency, allele frequency difference between cases and controls, and OR, respetively;
column 12-14 is the asymptotic standard deviation (SD) of the ascertainment-corrected mle for allele frequency, allele frequency difference between cases and controls, and OR, respetively.