IQLS: Haplotype Analysis for Case-Control Samples with Related Individuals
Version 1.2 March 9, 2011
Copyright(C) Zuoheng Wang
Mary Sara McPeek
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
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
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.
Download the software