###-  HapMap individual genotypes -### 

This directory contains datafiles with genotypes on all SNPs
produced by HapMap genotyping centers, and more recently, other
independent sources, such as Affymetrix and Illumina, and submitted 
to the DCC. Genotypes correspond to the four HapMap populations: 
90 Caucasian individuals from 30 CEPH family trios, 90 individuals 
from 30 family trios from the Ibadan people (Nigeria, West Africa), 
and 90 unrelated individuals from Southeast Asia (45 Han Chinese from 
Beijin, and 45 Japanese from Tokyo).

See project website (http://www.hapmap.org) for further information 
on samples and overall scientific goals.

Data files are available for bulk download from this directory. Another 
way to retrieve data is to browse a genomic region in the GBrowse 
viewer on the project website (http://www.hapmap.org/cgi-perl/gbrowse)
and then use the SNP Genotype Data dumper plugin. A third way to download 
genotying data is to use the Genotype attributes page of the HapMart 
application at http://hapmart.hapmap.org/BioMart/martview

File format. In general, genotype files consists of tab-delimited text 
files with at least the following columns:

Col1: refSNP rs# identifier at the time of release (NB might merge 
      with another rs# in the future)
Col2: SNP alleles according to dbSNP
Col3: chromosome that SNP maps to 
Col4: chromosome position of SNP, in basepairs on reference sequence
Col5: strand of reference sequence that SNP maps to
Col6: version of reference sequence assembly
Col7: HapMap genotype center that produced the genotypes
Col8: LSID for HapMap protocol used for genotyping
Col9: LSID for HapMap assay used for genotyping
Col10: LSID for panel of individuals genotyped
Col11: QC-code, currently 'QC+' for all entries (for future use)
Col12 and on: observed genotypes of samples, one per column, sample 
identifiers in column headers (Coriell catalog numbers, example: 
NA10847). Duplicate samples have .dup suffix.


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