SNaP

SNaP is a simulation program for haplotypic and genotypic data of single nucleotide polymorphisms (SNP). It assumes the SNP sequence to consist of one or more independent haplotype blocks. Each block can contain a causative SNP that affects an optional phenotypic expression, i.e. either a qualitative trait (affection status) or a quantitative trait (QT). These can be used, for example, in haplotype-based association analysis and in QTL analysis. The program has the following features:

Design: Unrelated individuals or nuclear families with a fixed or random number of children, optional separate sampling of cases and controls in association studies

Model: Phenotype definition dependent on the genotypic state of one or more causative SNP loci, according to specified penetrance values (affection status) or to Gaussian distributions with specified mean values and a homoscedastic variance

Output: various output formats, including Linkage format

Miscellaneous: missing data/random generation of genotyping errors, omission of causative SNPs from the data set, random generation of haplotypes within blocks, check for bi-allelic SNPs in the specified block haplotypes

Technical: use of job settings files, adaptable to memory consumption and languages (job settings files)

When you use SNaP in publications, please cite the following reference: Nothnagel M (2002). Simulation of LD block-structured SNP haplotype data and its use for the analysis of case-control data by supervised learning methods. Am J Hum Genet 71 (Suppl.)(4):A2363.

Cologne Center for Genomics | Statistical Genetics and Bioinformatics | Web interface written by S.Köhler, H.Rohde | state 2014