VarIBD
SAS macro that estimates the variance of the mean identity by descent (IBD) via a bootstrap method adapted for nonparametric linkage settings. Accompanying SAS macro will also test for homogeneity of mean IBD across different linkage datasets (or subsets within the same dataset) using the DerSimonian and Laird random effects model.
Where to get it:
The macro is available from Matt McQueen upon request.
References:
(1) McQueen MB, Blacker DB, Laird NM (2006). Variance calculations for identity-by-descent estimation. Am J Hum Genet 78:914-921.
FBAT
The Family-Based Association Test (FBAT) package is developed and maintained by Dr Nan Laird at the Harvard School of Public Health. FBAT is a generalized extension of the transmission disequilibrium test (TDT) that can accommodate a variety of family-based data including trios, sibling pairs and larger nuclear families. It can analyze data from It is one of the most widely used family-based association packages. It is available at no cost through the FBAT webpage.
Where to get it:
References:
(1) Rabinowitz D and Laird NM (2000) A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information. Human Heredity 504:227-233.
(2) Laird NM, Horvath S and Xu X (2000) Implementing a unified approach to family based tests of association. Genetic Epi 19(Suppl 1): S36-S42.
PBAT
PBAT developed out of the FBAT framework and is maintained by Dr Christoph Lange at the Harvard School of Public Health. Compared to FBAT, PBAT deals with more complicated scenarios typically encountered in genome-wide association studies including an approach to address extreme multiple testing scenarios. In addition, PBAT has the most extensive suite of tools to deal with highly dimensional phenotypic data in the family-based association framework. Note that PBAT is also a no-cost package and a graphical interface has been developed as a R package known as P2BAT (maintained and developed by Thomas Hoffmann).
Where to get it:
P2BAT R GUI: http://www.people.fas.harvard.edu/~tjhoffm/pbatR.html
References:
(1) Lange C, DeMeo D, Silverman E, Weiss S and Laird NM (2004) PBAT: tools for family-based association studies Am J Hum Genet 74:367-9.
(2) Van Steen K, McQueen MB, Herbert A, Raby B, Lyon H, Demeo DL, Murphy A, Su J, Datta S, Rosenow C, Christman M, Siverman EK, Laird NM, Weiss ST, Lange C (2005) Genomic screening and replication using the same data set in family-based association testing. Nat Genet 37:683-691.
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