Exploring Genetic Variation with SNaP

SNaP is a simulation program for haplotypic and genotypic data of single nucleotide polymorphisms (SNPs)

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SNaP stands as a robust simulation program designed for the analysis of haplotypic and genotypic data related to single nucleotide polymorphisms (SNPs).

It operates on the assumption that SNPs occur in one or more independent haplotype blocks, i.e., genomic regions that are not correlated with each other (no linkage disequilibrium).

Each of these blocks may harbor a causative SNP that can influence an optional phenotypic expression. This expression can manifest as either a qualitative trait (affection status) or a quantitative trait (QT). These features find application in diverse scenarios, ranging from the exploration of haplotype-based analyses to QTL (Quantitative Trait Locus) analyses.

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The program boasts the following key 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.

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Data Design

Number of Study Units

Number of individuals
Number of cases
Number of case controls
Number of families
Number of Children

Sex and Age Distribution Data

Sex Ratio
Age Range
to
Age Distribution
Age Mean
Age Standard Deviation
Age at First Child (Mother)
Age Standard Deviation (Mother)
Parental Age Difference
Parental Age Difference Standard Deviation
Minimum Child Age Distribution

Data Model

Haplotype Blocks

Please specify the Haplotype Blocks constituting the SNP Sequence

Data Output

Please specify the Parameters for the Data Output

File names
Settings file to be used with SNaP
Data file (generated by SNaP)
Settings file (potentially containing modified parameters)
Type of genotypic output
Information
Format:
Separators
Behind status column:
Between haplotypes:
Between blocks:
Between SNPs