QTDT - Multiple Alleles
By default QTDT analyses each marker allele separately. In
some situations this can result in a very large number of tests,
making it difficult to assess the value of significant associations.
A global p-value can be calculated for microsatellite marker
alleles using the --multi-allelic option with the orthogonal
family of tests (-af, -ao, -ap, -at). When this option
is used, rare alleles (with a frequency <= 5% in the total
genotyped sample) are lumped together and individual effects for
all other alleles are estimated producing a single p-value per
marker / phenotype pair.
For example, this option could be used as follows:
prompt> qtdt -d microsat.dat -p microsat.ped --multi -ao -wega
(Note that long option names can be abbreviated, so that --multi
and --multi-allelic are equivalent)