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- Marker Names (Optional; string) The first row in the file
can contain a list of identifiers for each of the markers in the data
set. This row contains strings of integers or characters, where
is the number of loci.
- Inter-Marker Distances (Optional; real) the next row in the
file is a set of inter-marker distances, for use with linked loci.
These should be genetic distances (e.g., centiMorgans), or some proxy
for this based, for example, on physical distances. The actual units
of distance do not matter too much, provided that the marker distances
are (roughly) proportional to recombination rate (the algorithm
estimates an appropriate scaling from the data).
The markers must be in map order within linkage groups. When
consecutive markers are from different linkage groups (e.g., different
chromosomes), this should be indicated by the value -1. The first
marker is also assigned the value -1. All other distances are
non-negative. This row contains real numbers.
- Individual Data (Required) Data for each sampled individual is
arranged into one or more rows as described above (further details
below).
- Phase Information (Optional; diploid data only; real number
in the range [0,1]). This is for use with linked loci only. This is
a single row of probabilities that appears after the genotype data
for each individual. If phase is known completely, or no phase
information is available, these rows are unnecessary. They may be
useful when there is partial phase information from family data. There
are two alternative representations for the phase information: (1) the
two rows of data for an individual are assumed to correspond to the
paternal and maternal contributions, respectively. The phase line
indicates the probability that the ordering is correct at the current
marker; (2) the phase line indicates the probability that the phase of
one allele relative to the previous allele is correct. The first entry
should be filled in with 0.5 to fill out the line to entries.
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William Wen
2002-07-18