Sib-pair Command: read hapmap


ClassData Declaration command
Nameread hapmap
Arguments <data file name>

Reads a HapMap style genotypes data file. All individuals are assumed unrelated.

The HapMap genotype file genotype is tab delimited with (usually):

ColumnDescription
1 refSNP rs number identifier at the time of release (NB might merge with another rs number in the future)
2dbSNP SNP alleles
3chromosome
4Position (bp)
5strand
6assembly version
7HapMap genotyping center
8LSID for HapMap protocol
9LSID for HapMap assay
10LSID for panel of individuals genotyped
11QC-code
12 and onobserved genotypes of samples, one per column, sample identifiers in column headers (Coriell catalog numbers, example: NA10847). Duplicate samples have .dup suffix.

Example:

>> read hap genotypes_chr15_CEU_r27_nr.b36_fwd.txt.gz
Pedigree file         = genotypes_chr15_CEU_r27_nr.b36_fwd.txt
Number of loci        = 108464
Number of individuals = 174
Number of genotypes   = 18872736
Read in  174 pedigrees, 174 individuals
         12671030 nonmissing SNP genotypes (56.04 s)
Dataset occupies 75.506 Mb.

See also:

read pedigree read Sib-pair pedigree file
read linkage read pre-Makeped pedigree file
read ppd read post-Makeped pedigree file


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