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SNaP: Simulation of SNP haplotype data and phenotypic traits
| Description of the program |
| Web Interface / Obtaining SNaP / Downloads |
| Citation & Feedback |
| Job file example for use with SNaP |
Description of the program
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 | |
||
| 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
| [General] | ||
| DataFilename | = | 'expl.dat' |
| SettingsFilename | = | 'expl.set' |
| OutputType | = | 'haplotypes' |
| OutputFormat | = | 'Standard1' |
| [Design] | ||
| TypeOfPhenoExpression | = | 'qualitative' |
| StudyDesign | = | 'individuals' |
| SamplingDesign | = | joint' |
| NumberOfIndividuals | = | 1000 |
| [Model] | ||
| NumberOfLoci | = | 1 |
| NumberOfStates | = | 3 |
| Penetrances | = | |
| 1.0 0.5 0.0 | ||
| BiallelicCheck | = | 'y' |
| RemoveCausalSNPs | = | 'n' |
| GenotypingError | = | 0.010 |
| GenotypingErrorVisible | = | 'y' |
| RandomSeed | = | 500 |
| [Separators] | ||
| BehindStatus | = | '\t' |
| BetweenHaplotypes | = | ' ' |
| BetweenBlocks | = | '.' |
| BetweenSNPs | = | '' |
| [Blocks] | ||
| NumberOfBlocks | = | 2 |
| (Block) | ||
| Number | = | 1 |
| Size | = | 3 |
| SuscLocusPosition | = | 2 |
| SuscAlleleFrequ | = | 0.200 |
| {NoSuscHaplotypes} | ||
| HtNumber | = | 2 |
| HtBlock | = | 111 |
| HtBlock | = | 211 |
| HtFrequ | = | 0.60 |
| {SuscHaplotypes} | ||
| HtNumber | = | 3 |
| HtBlock | = | 122 |
| HtBlock | = | 221 |
| HtBlock | = | 22 |
| HtFrequ | = | 0.30 |
| HtFrequ | = | 0.50 |
| (Block) | ||
| Number | = | 2 |
| Size | = | 1 |
| SuscLocusPosition | = | 0 |
| {NoSuscHaplotypes} | ||
| HtNumber | = | 2 |
| HtBlock | = | 2 |
| HtFrequ | = | 0.70 |
| Last update: December 14, 2005 | Visitors since 11/11/2003:
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