User Guide for HaploShare (v1.01)
please contact me if you have any problems (jonsonfox@gmail.com)

For quick test, please type:  HaploShare -file 300test -ch 1 -perm 100 -cut 1 -out test

Outline
I.	System requirement  
II.	Input file format
III.	Output file format
IV.	Data preparation process
V.	Effective commend
VI.	Updates


I.	System requirement  
	Current version of HaploShare only supports windows system (better for 64bit windows 7 ). 
	The minimum memory required is 4GB (500 samples) and 8GB is recommended (1000 samples) 
	Make sure that perl is installed and added into the system default path.
	Make sure that PLINK is installed and added into the system default path.

II.	Input file format
	The input file format is the binary plink format, including
		.bim file	(map file)
		.bed file	(binary genotype file)
		.fam file	(sample information file, including case and controls)
III.	Only one output file will be generated. Each line describing the details of a IBD sharing region as follows.
		chromosome			
		number of samples in this IBD region
		physical length of the region (by kb)
		first position of the IBD region (start of partially shared region,please refer to the paper.) (by bp)
		last position of the IBD region]
		number of SNPs in the IBD region
		permutated P value
		order of the samples share this IBD region. (1,2,3...n, n=sample size).
		first and last SNP index of each samples in the IBD region
		sharing haplotype of the IBD region (by SNP, 0 for common SNP and 1 for rare SNP, blocks are separated by "|", "-" are the SNPs between blocks)
		frequency for the sharing haplotype in the IBD region.
		start and end position of shared haplotype for each sample in the region.

IV.	Data preparation process
		The input data should be prepared by the following process
		1	perl to22.pl -i yourfilename				// all the data will be separated into single chromosomes. It will be easy for pararellel analysis.
											//*(if the data is in only one chromosome, please omit this step. The testing data is only chromosome 1.)
		2	PhaseToBlockFrequency -i yourfilename	//phasing precedure

V.	Effective commend
		The main program (HaploShare.exe) have the following commends:
		-file		input file name (without file format extensions)
		-chr		chromosome index, from 1 to 22, type "all" if analysing all the chromosomes
		-perm	number of permutation process (defult 1000)
		-cut		length cutoff for pairwise IBD detection (defult 1 cM)
		-out		output file name

		exmple:

		HaploShare -file 300test -ch 1 -perm 100 -cut 1 -out test

VI.	Updates
		source code for the main program "HaploShare was released in 15th Sep. 2012".
		souce code for the appendant program "PhaseToBlockFrequency" will be released soon.