IQLS 1.2 – Haplotype Analysis for Case-Control Samples with Related Individuals

IQLS 1.2


IQLS  (Incomplete-Data Quasi-likelihood Score Test) 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.



Zuoheng Wang and Mary Sara McPeek




  • Linux /  Windows / MacOsX
  • C Compier





Wang, Z., and McPeek,M.S. (2009).
An incomplete-data quasi-likelihood approach to haplotype-based genetic association studies on related individuals.
J. Am. Stat. Assoc. 104, 1251-1260.

Wang, Z., and McPeek, M.S. (2009).
ATRIUM: Testing untyped SNPs in case-control association studies with related individuals.
Am. J.Hum. Genet. 85, 667-678.

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