Snpmstat

Record added by Jurg Ott (the original Rockefeller list)

SNP Missing data STATistics

4.0

SNPMStat is a command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to estimate or test SNP effects and SNP-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty, study design and gene-environment dependence. For SNPs without missing data, the program performs the standard association analysis. For typed SNPs with missing data or untyped SNPs, the program performs the maximum-likelihood analysis.

Danyu Lin’s group (Univ North Carolina)

http://www.bios.unc.edu/~lin/software/SNPMStat/

Lin, Hu, Huang (2008), “Simple and efficient analysis of SNP-disease association with missing genotype data”, American Journal of Human Genetics, 82:444-452.