Genome-wide Association Simulator - Output Formats for Case-Control

This page describes output formats for case-control
  In all instances, 0 represents the major allele, 1 represents the minor allele. Genotypes are coded as the number of minor alleles, so genotypes can assume the values 0,1, or 2.

Suppose a user asks for n cases or controls. The haplotype output format would be: 
column 1: chromosome number 
column 2: SNP ID
column 3: physical location of the SNP
column 4: minor allele frequency of the SNP in HapMap CEU trios
column 5 through 2n + 4: haplotypes
An example with 5 SNPs, 10 controls, on chromosome 10: 
10	rs1247696	29826038	0.01666667	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
10	rs6481613	29831217	0.41666667	1	1	0	1	0	1	0	1	0	1	0	1	0	0	1	0	0	0	1	1
10	rs2182402	29835030	0.41666667	1	1	0	1	0	1	0	1	0	1	0	1	0	0	1	0	0	0	1	1
10	rs4747667	29840416	0.36666667	1	1	0	0	0	1	0	1	0	1	0	1	0	0	1	0	0	0	1	1
10	rs3740003	29844044	0.25000000	1	1	1	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	1
The genotype output format would be: 
column 1: chromosome number 
column 2: SNP ID
column 3: physical location of the SNP
column 4: minor allele frequency of the SNP in HapMap CEU trios
column 5 through n + 4: genotypes
The same example with 5 SNPs, 10 controls, on chromosome 10: 

10	rs1247696	29826038	0.01666667	0	0	0	0	0	0	0	0	0	0
10	rs6481613	29831217	0.41666667	2	1	1	1	1	1	0	1	0	2
10	rs2182402	29835030	0.41666667	2	1	1	1	1	1	0	1	0	2
10	rs4747667	29840416	0.36666667	2	0	1	1	1	1	0	1	0	2
10	rs3740003	29844044	0.25000000	2	1	0	0	1	0	0	1	0	1
 
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