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	INFORMATION FOR THE FILES CONTAINED IN THIS DIRECTORY.
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- Folders YRI and CEU in this directory contain the phased haplotypes from the consensus HapMap III data,
  		of populations YRI and CEU respectively.


 	- Files are compressed and have filenames of the form: hapmap3_r2_b36_fwd.consensus.qc.poly.chrX_Y.phased.gz
		where X is the chromosome number and Y the three letter abbreviation for the population the samples belong to (in lower case)
		e.g.: hapmap3_r2_b36_fwd.consensus.qc.poly.chr20_ceu.phased.gz


	- Files are organised in a snps x haplotypes format, so every row represents a SNP and every column a haplotype.

		- The first row (header row) contains the IIDs of the individuals that have been phased.
  	  		Suffixes _A and _B represent transmitted and untransmitted alleles, respectively,for a particular genotype. 
  	  		For instance, NA19009_A would be the transmitted allele of genotype NA19009 at that site.

		- The first column (header column) contains the rsID of the SNPs were the individual genotypes have been typed. 

		- The second column contains the physical position of these SNPs in the particular chromosome.

		- Entries with anything other than A, C, G, or T represent unresolved haplotypes.


- The imputation of unresolved alleles in these files was performed using Bryan Howie's algorithm (impute++).

	- The recombination rates used are from  22_b36 release of Hapmap data and can be found online at:
		http://ftp.hapmap.org/recombination/2008-03_rel22_B36/rates/

	- Effective population size used for CEU is  11418

	- Effective population size used for YRI is  17094