| Class | Data Declaration command |
| Name | read 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):
| Column | Description |
|---|---|
| 1 | refSNP rs number identifier at the time of release (NB might merge with another rs number in the future) |
| 2 | dbSNP SNP alleles |
| 3 | chromosome |
| 4 | Position (bp) |
| 5 | strand |
| 6 | assembly version |
| 7 | HapMap genotyping center |
| 8 | LSID for HapMap protocol |
| 9 | LSID for HapMap assay |
| 10 | LSID for panel of individuals genotyped |
| 11 | QC-code |
| 12 and on | observed 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 |
| << (read vcf) | Up to index | >> (read bin) |