ROADTRIPS 2.0 is a C program that performs single-SNP, case-control association testing in samples with partially or completely unknown population and pedigree structure. The main reference for this program is Thornton T., McPeek M. S. "ROADTRIPS: Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure" (2010) American Journal of Human Genetics, vol 86, pp. 172-184. ROADTRIPS uses an empirical covariance matrix calculated from genomewide SNP data to correct for unknown population and pedigree structure, while maintaining high power by taking advantage of known pedigree information when it is available. The program is applicable to association studies with completely general combinations of related and unrelated individuals. Analysis can be performed genomewide (currently just for autosomes).

ROADTRIPS is suitable for applications such as:

• correcting for possible population structure and/or misspecified relationships in the context of case-control association testing in samples of unrelated individuals and/or related individuals with well-characterized pedigrees
  
  
• case-control association testing in samples from isolated populations for which pedigree information is limited or unavailable

With Partial or Complete Pedigree Information:

Although no pedigree information is needed to run ROADTRIPS, when partial or complete pedigree information is available, it is desirable to incorporate this information into the analysis to improve power. In ROADTRIPS, this is done by inputting working kinship and inbreeding coefficients calculated from available pedigree information. A software program that can be used to obtain kinship and inbreeding coefficients from pedigree data is

(1) The KinInbcoef software of Catherine Bourgain and Qian Zhang. The output file of the KinInbcoef program has the exact format needed for the ROADTRIPS software.