SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values

Table 1 Characteristics of three software that simulate marker data under non-null genetic models.

	SLINK/SUP	SIMLA	ALLEGRO
Simulates on pedigrees as they have been collected	Yes	No	Yes
Simulates marker data conditional on
1) observed affection status	Yes	Yes	Yes
2) observed affection status and observed exposure/liability class	Yes	No	No
3) observed quantitative trait values	Yes	No	No
Simulates LD between
1) marker loci	Yes	Yes	No
2) marker and trait loci	Yes	Yes	No
Simulates values for
1) affection status	Yes	Yes	No
2) environmental exposure	No	Yes	No
3) quantitative trait	Yes	Yes	No
4) covariates	No	Yes	No
Simulates multi-locus susceptibility between
1) unlinked loci	Yes (indirectly)	Yes	No
2) linked loci	No/Future	Yes	No
Simulates under sex-specific maps	Yes	No	Yes
Simulates X-linked genetic data	Yes/Future	No	Yes
Simulates upon pedigrees with loops	Few	No	Yes
Pedigree restrictions	16 founders	4 founders	< 31 bits^†

Some features are planned future extensions of SUP. ^†The number of bits is defined as twice the number of non-founders minus the number of founders.

ISSN: 2730-6844