:: DESCRIPTION
SNPCaller (Smarter Clustering Methods for SNP Genotype Calling) is a set of routines for making genotype calls from raw intensity data using mixture models for disomic or trisomic data
::DEVELOPER
Division of Statistical Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yan Lin et al.
Smarter clustering methods for SNP genotype calling
Bioinformatics (2008) 24 (23): 2665-2671.
:: DESCRIPTION
CNVEM is a Bayesian Expectation-Maximization algorithm that infers carrier status of CNVs in large samples from SNP genotyping data, such as are available in genome-wide association studies. Using Bayesian computations the program calculates the posterior probability for carrier status of known CNV in each individual of a sample by jointly analyzing genotype information and hybridization intensity. Signal intensity is modeled as a mixture of normal distributions, allowing for locus-specific and allele-specific distributions. Using an expectation maximization algorithm, these distributions are estimated and then used to infer the carrier status of each individual the boundaries of the CNV.
::DEVELOPER
Sebastian Zöllner @ the Center for Statistical Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
If you use CNVEM please e-mail szoellne@umich.edu or fill out the registration form.
:: DESCRIPTION
AssociationViewer is a Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.
::DEVELOPER
the Swiss Institute of Bioinformatics, Vital-IT group.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Olivier Martin, Armand Valsesia, Amalio Telenti, Ioannis Xenarios and Brian J. Stevenson
“AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context”
Bioinformatics (2009) 25 (5): 662-663.
:: DESCRIPTION
PolyPhred is a program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. PolyPhred is not a stand alone application. PolyPhred’s functions are integrated with the use of three other programs: Phred, Phrap, and Consed . PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.
::DEVELOPER
Dr. Deborah Nickerson’s lab at the University of Washington
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
PolyPhred is available for free to researchers at academic and non-profit institutions.
Commercial businesses wanting to acquire PolyPhred are required to purchase a commercial license agreement.
:: DESCRIPTION
The program sampletrees is a Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
sampletrees and Rsampletrees: Sampling gene genealogies conditional on SNP genotype data.
Burkett KM, McNeney B, Graham J.
Bioinformatics. 2016 Jan 18. pii: btv763.
