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HapMap Haplotypes for data release #22 (13/08/07) 
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The haplotypes for all the autosomes and chrX will be released as they are processed in the directories below

all/ consensus/ phased/ 

which contain 3 versions of the data we have created
 
phased/ contains the haplotypes for each panel but only at SNPs that are segregating in each panel
i.e. if a SNP does not segregate in the CEU panel then it is not included in the CEU haplotypes.
 
Each dataset has 3 files per chromosome/population panel. For example, for chr22 in the CEU panel there are the files

/phased/CEU/chr22/genotypes_chr22_CEU_r22_nr.b36_fwd_legend.txt
/phased/CEU/chr22/genotypes_chr22_CEU_r22_nr.b36_fwd_sample.txt
/phased/CEU/chr22/genotypes_chr22_CEU_r22_nr.b36_fwd_phased
 
The _legend.txt file contains a legend detailing the rs id, base pair position, the allele coded 0
and the allele coded 1 for each of the segregating SNPs e.g.
 
rs              position        0       1
rs11089130      14431347        C       G
rs738829        14432618        A       G
rs915674        14433624        A       G
 
The _phased contains the haplotypes arranged one haplotype per row.
 
For the CEU and YRI the haplotypes are arranged as follows:
 
row 1 - trio 1 parent 1 transmitted haplotype
row 2 - trio 1 parent 1 untransmitted haplotype
row 3 - trio 1 parent 2 transmitted haplotype
row 4 - trio 1 parent 2 untransmitted haplotype
row 5 - trio 2 parent 1 transmitted haplotype
row 6 - trio 2 parent 1 untransmitted haplotype
row 7 - trio 2 parent 2 transmitted haplotype
row 8 - trio 2 parent 2 untransmitted haplotype
.
.
 
For the JPT+CHB the haplotypes are arranged as
 
row 1 - individual 1 haplotype 1
row 2 - individual 1 haplotype 2
row 3 - individual 2 haplotype 1
row 4 - individual 2 haplotype 2
row 5 - individual 3 haplotype 1
row 6 - individual 3 haplotype 2
.
.
 
For chrX there are *non_par.phased, *par1.phased and *par2.phased files for non-pseudo autosomal region, 
first pseudo autosomal region and second pseudo autosomal region respectively. Files with haplotypes from 
the non-pseudo autosomal region have 2 lines per individual but males have only one haplotype with the 
other haplotype represented as a row of dashes (-). This makes the *sample.txt files match up with the 
haplotypes in a straight-forward way.

The _sample.txt file contains an ordered list of individual ids that corresponds to the _phased file. 
For the CEU and YRI panels the individual id's are arranged as follows but the _phased files do not 
contain the haplotypes of the children as these can be infered from the parents haplotypes
 
trio 1 parent 1
trio 1 parent 2
trio 2 parent 1
trio 2 parent 2
.
.
.
trio 30 parent 1
trio 30 parent 2
trio 1 child
trio 2 child
.
.
.
trio 30 child
 
/all contains the haplotypes for each panel with the monomorphic sites put back into the haplotypes.
Each panel has two files per chromosome/region. A _phased_all file that contains the haplotypes in the same
format as described above and a _legend_all file that contains the rs, position and allele coding
for each SNP in the haplotypes. SNPs that exist in multiple panels have the same coding of alleles.
 
/consensus - contains a set of haplotypes for each population at only those SNPs that are in all
3 panels. There is one _phased_consensus file that contains the haplotypes for each chromosome/region and
one _consensus_legend+freq for each chromosome/region that details rs, position, allele coded 0, allele coded 1,
CEU allele 1 count, YRI allele 1 count and JPT+CHB allele 1 count.