University of Michigan Center for Statistical 
Search Liming's website


The MQLS program for case-control association testing with related individals using genotype or allele dosage data

This website provides our implementation of the efficient method, MQLS, developed by Thornton and McPeek (2007). It can handle arbitrary number of markers and samples and have other features that we found useful in our studies, such as pedigree checking and input/output formats. In addition to genotyped markers, this version can carry out association tests using imputed allele counts ("dosages") generated by MACH and an empirical variance estimator. The program uses QTDT/MERLIN/LINKAGE format as the input format and outputs the association test results for each marker and affection status in a table format.
Comments and suggestions are appreciated. Please email me:
Pre-compiled and instruction downloads:
MQLS.tar.gz(64bit), MQLS_32bit.tar.gz (32bit)
MQLS_Mac.tar.gz (64bit), MQLS_Mac_32bit.tar.gz (32bit) (Thanks Xiaowei for making this available!), more trick for Mac user.


If you are using this package, please cite this website and the reference below.

Reference for the MQLS method:

Thornton T., McPeek M. S. (2007) Case-Control Association Testing with Related Individuals: A More Powerful Quasi-Likelihood Score Test. Am J Hum Genet, 81, 321-337.






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