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)