:: DESCRIPTION
ClusterA is a tool for calculating some statistics on clusters, the most important being the “Silhouette Score” used in our group for genotype cluster validation.
::DEVELOPER
Molecular Medicine research group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lovmar L, Ahlford A, Jonsson M, Syvänen A-C (2005)
Silhouette scores for assessment of SNP genotype clusters.
BMC Genomics 6:35
:: DESCRIPTION
SNPHAP is a program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects
::DEVELOPER
David Clayton (david.clayton@cimr.cam.ac.uk)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SNPflow is a freely available web application to automatically check the quality of SNP data employing the ABI 7900 HT-platform (e.g. TaqMan, KASPar Assays) or the Sequenom iPLEX platform: Single raw output files of plates are automatically merged and converted to genotype lists.
::DEVELOPER
GenEpi – Division of Genetic Epidemiology Innsbruck
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
SNPflow: a lightweight application for the processing, storing and automatic quality checking of genotyping assays.
Weissensteiner H, Haun M, Schönherr S, Neuner M, Forer L, Specht G, Kloss-Brandstätter A, Kronenberg F, Coassin S.
PLoS One. 2013;8(3):e59508. doi: 10.1371/journal.pone.0059508.
:: DESCRIPTION
QCTOOL is a command-line utility program for basic quality control of gwas datasets. It supports the same file formats used by the WTCCC studies, as well as the binary file format described here, and is designed to work seamlessly with SNPTEST and related tools. QCTOOL computes per-sample and per-SNP summary statistics, and uses these to filter out samples and SNPs from the dataset (either by removing them from the files or by writing exclusion lists).
::DEVELOPER
Gavin Band , Jonathan Marchini
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SSEA (SNP Set Enrichment Analysis) is a new SNP-based pathway analysis software for GWAS studies. SSEA consists of two main steps: selecting representative SNPs for each gene, and performing pathway enrichment analysis using all selected SNPs.
::DEVELOPER
CBCL Lab (Computational Biology and Computational Learning) @ UCI
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lingjie Weng, Fabio Macciardi, Aravind Subramanian, Guia Guffanti, Steven G. Potkin, Zhaoxia Yu, Xiaohui Xie
“SNP-based Pathway Enrichment Analysis for Genome-wide Association Study“;
BMC Bioinformatics 2011, 12:99
:: DESCRIPTION
SNPsetter is a program for manipulating Affymetrix SNP metadata. SNPsetter will filter the SNPs exported, by chromosome, by allele frequency, or by distance from the last-exported SNP.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Mutat. 2009 Jun;30(6):960-7. doi: 10.1002/humu.20974.
IBDfinder and SNPsetter: tools for pedigree-independent identification of autozygous regions in individuals with recessive inherited disease.
Carr IM, Sheridan E, Hayward BE, Markham AF, Bonthron DT.
:: DESCRIPTION
IBDFinder aids the identification of regions of Identity By Descent (IBD) in inbred individuals, by plotting and collating runs of homozygous SNP genotypes, ordered by physical or genetic distance.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Mutat. 2009 Jun;30(6):960-7. doi: 10.1002/humu.20974.
IBDfinder and SNPsetter: tools for pedigree-independent identification of autozygous regions in individuals with recessive inherited disease.
Carr IM, Sheridan E, Hayward BE, Markham AF, Bonthron DT.
:: DESCRIPTION
DominantMapper is a method for identifying linkage to dominant genes in a single pedigree where there is SNP data for at least one pair of parents (one of whom is affected). Linkage information is then extrapolated from the genotypes of their affected and unaffected children as well as other affected relatives.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Mutat. 2011 Dec;32(12):1359-66. doi: 10.1002/humu.21597. Epub 2011 Sep 19.
DominantMapper: rule-based analysis of SNP data for rapid mapping of dominant diseases in related nuclear families.
Carr IM, Johnson CA, Markham AF, Toomes C, Bonthron DT, Sheridan EG.
:: DESCRIPTION
AutoSNPa aids the identification of regions of Identity By Descent (IBD) in inbred families, by visually presenting colour-coded SNP genotype data ordered by physical or genetic distance.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Mutat. 2006 Oct;27(10):1041-6.
Interactive visual analysis of SNP data for rapid autozygosity mapping in consanguineous families.
Carr IM, Flintoff KJ, Taylor GR, Markham AF, Bonthron DT.
:: DESCRIPTION
AgileGenotyper will create a pseudo-microarray SNP genotyping file from an ordered SAM file containing exon sequence data. The file will contain the genotype data at over 0.5 million SNP sites previously identified by the 1000 Genomes project. Such a file can then be used as a data source for a mapping program designed for analyzing Affymetrix microarray SNP data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
