SNaP: Simulation of SNP haplotype data and phenotypic traits

Description of the program

• The SNaP program can be used to generate SNP haplotype sequence data of unrelated individuals and nuclear families with a fixed or random number of children.
• It assumes the SNPs to occur in disjoint blocks with limited numbers of haplotypes each.
• If required each block can contain a trait-causative SNP. Each individual is then randomly assigned an affection status or a quantitative trait conditional on the one or more causative SNPs' genotypes according to specified penetrances or mean effects, respectively.
• Cases and controls can optionally be sampled separately; otherwise individuals and families are sampled jointly.
• Haplotypes are independently sampled in each block and subsequently concatenated to form the sequence haplotype. Haplotype frequencies and SNP alleles can either be specified block-wise or are randomly generated otherwise.
• The program allows for missing data, genotyping errors, omission of causative SNPs from the output and strictly bi-allelic or possibly mono-allelic SNP markers.
• It uses job files and is adaptable to memory consumption; characters and designators can be modified, e.g. adapted to different languages.
• A log output file contains the parameters used for the data generation, including program-generated block haplotypes and frequencies. The data file contains the generated individuals/families in one of various formats, e.g. Linkage format.
• The program suggests valid values for erroneously specified parameters. Several job-settings examples are provided.

A poster was presented at the ASHG meeting in 2002.
A more detailed documentation can be downloaded.

Web Interface / Obtaining SNaP / Downloads

SNaP was written in ANSI-C and is distributed under the GNU General Public License (see www.gnu.org for details).

SNaP can be used with a Web Interface. The interface allows for a comfortable creation of job settings files and the succeeding generation of the data set. Both files can be downloaded. For the generation of a higher number of data sets and for automated processing in simulation studies, the SNaP program can be downloaded and be installed on a local computer.

The following files are available for download:

	Description	File	Size	Format	Useful software
	SuSE Linux executable	snap.suse	67 kB	binary
	RedHat Linux executable	snap.redhat	70 kB	binary
	Sun Solaris executable	snap.sun	91 kB	binary
	Windows/DOS executable	snap.exe	82 kB	binary
	Program documentation	snap.pdf	254 kB	PDF
		snap.ps	1.4 MB	PostScript
		snap.ps.gz	468 kB	Zipped PostScript
		snap.ps.zip	475 kB	Zipped PostScript
	Short sources installation guide	install.txt	3 kB	ASCII text
	BibTeX citation file	snapref.bib	4 kB	BibTeX
	GNU General Public License	gpl.txt	18 kB	ASCII text

To obtain the software sources, please send me an e-mail with subject "SNaP request" to nothnagel medinfo.uni-kiel.de.

Citation & Feedback

Please cite the following reference when reporting the results using SNaP:

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.

Comments and error feedback are appreciated. Please send an e-mail to nothnagel medinfo.uni-kiel.de with subject: "Comment on SNaP".

Job file example to be used with SNaP