fastStructure 1.0 – Inferring Population Structure from SNP Genotype data

fastStructure 1.0

:: DESCRIPTION

fastStructure is an algorithm for inferring population structure from large SNP genotype data.

::DEVELOPER

Pritchard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python
  • Numpy
  • Scipy
  • Cython
  • GNU Scientific Library

:: DOWNLOAD

 fastStructure

:: MORE INFORMATION

Citation

fastSTRUCTURE: variational inference of population structure in large SNP data sets.
Raj A, Stephens M, Pritchard JK.
Genetics. 2014 Jun;197(2):573-89. doi: 10.1534/genetics.114.164350

ClusterA 1004 – Calculating Silhouette scores for Assessment of SNP Genotype Clusters

ClusterA 1004

:: 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

  • Windows

:: DOWNLOAD

 ClusterA

:: 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

SNPHAP 1.3.1 – Estimate Frequencies of Haplotypes of SNPs

SNPHAP 1.3.1

:: 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

  • Linux/WIndows
  • C Compiler

:: DOWNLOAD

  SNPHAP

:: MORE INFORMATION

SNPflow 1.3.5 – SNP Workflow Manager

SNPflow 1.3.5

:: 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

  • Windows/Linux
  • JRE

:: DOWNLOAD

 SNPflow

:: 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.

QCTOOL 2.0.8 – SNP Quality Control (QC) for Genome-wide Association Studies

QCTOOL 2.0.8

:: 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

  • MacOsX /  Linux

:: DOWNLOAD

 QCTOOL

:: MORE INFORMATION

SSEA 1.0 – SNP Set Enrichment Analysis for Genome-wide Association Studies

SSEA 1.0

:: 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

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 SSEA

:: 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

SNPsetter 20101215 – Standardization of SNP data

SNPsetter 20101215

:: 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

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 SNPsetter

:: 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.

IBDfinder 20121128 – Visual display of homozygous regions in SNP data files

IBDfinder 20121128

:: 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

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

  IBDfinder

:: 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.

DominantMapper 20110207 – Analysis of SNP data for rapid Mapping of Dominant Diseases in related Nuclear Families

DominantMapper 20110207

:: 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

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 DominantMapper

:: 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.

AutoSNPa 20121128 – Visual analysis of SNP data for autozygosity Mapping

AutoSNPa 20121128

:: 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

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AutoSNPa

:: 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.