SNAP Software V3.2 by Statistical Genetics and Bioinformatics Group - CCG

SNaP is a simulation program for haplotypic and genotypic data of 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/PLINK 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

Phenotype: type of trait

Model type

Sampling Design: type of sampling

Age Data

Age range (minimum – maximum allowed age)

Min Age: 1

Max Age: 100

Type of age distribution

Mean value of age distribution

Standard deviation of age distribution

Sex Data

Sex ratio males/females

Mean value of age difference father – mother

Standard deviation of age difference father – mother

Mean value of maternal age at first child

Standard deviation of maternal age at first child

Minimal age difference between consecutive children (occurs only with two or more children)

Study Design: type of study units

Family type

Number of families

Number of children

Number of cases

Number of controls

individuals

Phenotype Model

Number of SNP loci that affect the phenotype (causative loci)

Number of states

Should all SNPs be required to be heterozygous in the sample?

Should genotyping errors be marked in the sample?

Should causative SNPs be removed from the sample?

Probability of a genotyping error per SNP

Genotype Model (Haplotype Blocks)

Please specify the Haplotype Blocks constituting the SNP Sequence

Block contain a phenotype-affecting (causative) SNP

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

Generate only settings file

Exploring Genetic Variation with SNaP

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