IQLS is a C++ program that performs haplotype frequency estimation and case-control association testing between a binary trait and haplotypes of multiple tightly-linked SNPs. A special feature of IQLS is that both related and unrelated individuals can be included in the case-control sample. The user specifies the number of SNPs in the sliding haplotype window, and for each set of SNPs, the IQLS program computes haplotype frequency estimates and both 1-df and full-df tests for haplotype association with a case-control phenotype. The IQLS software is suitable for case-control haplotype analysis in outbred samples with arbitrary combinations of related and unrelated individuals, including large pedigrees, provided that the relationships are known.

The reference for the IQLS haplotype estimation methods and full-df IQLS haplotype association tests is Wang and McPeek (2009a) JASA 104:1251-1260, while the reference for the 1-df IQLS haplotype association tests is Wang and McPeek (2009b) AJHG 85:667-678 [see test (3) in subsection "Comparison to other approaches for related individuals"]. The IQLS haplotype estimation and testing methods can be considered extensions of the single-marker estimation and testing methods of McPeek, Wu, and Ober (2004) Biometrics 60:359-367, and Thornton and McPeek (2007) AJHG 81:321-337, respectively.

Note: The IBD coefficient file, one of the required input files to IQLS, can be obtained by running Mark Abney's IdCoefs software, which computes condensed identity coefficients for pairs of individuals within each family. The output of IdCoefs can be directly used as the IBD coefficient input file for IQLS.