Tag: HapMap

HAPMIXMAP 1.0 – Model HapMap Haplotypes

HAPMIXMAP 1.0

:: DESCRIPTION

HAPMIXMAP is a program for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program developed by Scheet and Stephens (2006).  The program models unphased genotype data on unrelated individuals, and fits a model in which linkage disequilibrium is generated by K independent Poisson arrival processes corresponding to K modal haplotype states.  This corresponds to the observation that typically 2-4 common haplotypes account for most of the allelic diversity in any haplotype block, and that rarer haplotypes are typically slight variants of these modal haplotypes.  The block-like structure of haplotypes in the genome, corresponding to ancestral recombination hotspots, is modelled by allowing the arrival rate to vary across the genome.

::DEVELOPER

Paul McKeigue

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HAPMIXMAP

:: MORE INFORMATION

ssSNPer 20070329 – Identify statistically similar SNPs (ssSNPs) in the HapMap

ssSNPer 20070329

:: DESCRIPTION

ssSNPer is a novel user-friendly web interface that provides easy determination of the number and location of untested HapMap SNPs, in the region surrounding a tested HapMap SNP, which are statistically similar and would thus produce comparable and perhaps more significant association results.

::DEVELOPER

the Statistical and Genomic Epidemiology Laboratory (SGEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux

:: DOWNLOAD

 ssSNPer

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Dec 1;22(23):2960-1. Epub 2006 Oct 12.
ssSNPer: identifying statistically similar SNPs to aid interpretation of genetic association studies.
Nyholt DR.

HapZipper – Compression Scheme for HapMap Phase III Phased Data

HapZipper

:: DESCRIPTION

HapZipper is a lossless compression tool tailored to compress HapMap data beyond benchmarks defined by generic tools such as gzip, bzip2 and lzma.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 HapZipper

:: MORE INFORMATION

Citation

HapZipper: sharing HapMap populations just got easier.
Chanda P, Elhaik E, Bader JS.
Nucleic Acids Res. 2012 Nov 1;40(20):e159. doi: 10.1093/nar/gks709.

HapMap filter 1.0 – Preprocess the HapMap Genotypic data for Association Studies

HapMap filter 1.0

:: DESCRIPTION

HapMap filter is a tool to preprocess the HapMap genotypic data for association studies.

::DEVELOPER

Dr. Wei Zhang, wzhang1@uchicago.edu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • C++ Compiler

:: DOWNLOAD

 HapMap filter

:: MORE INFORMATION

Citation

HapMap filter 1.0: a tool to preprocess the HapMap genotypic data for association studies.
Zhang W, Duan S, Dolan ME.
Bioinformation. 2008 May 13;2(8):322-4.

SNAP 2.2 – Identification and Annotation of proxy SNPs using HapMap

SNAP 2.2

:: DESCRIPTION

SNAP is a web server for finding and annotating proxy SNPs based on linkage disequilibrium, genomic location, and coverage by commercial genotyping arrays.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Johnson, A. D., Handsaker, R. E., Pulit, S., Nizzari, M. M., O’Donnell, C. J., de Bakker, P. I. W.
SNAP: A web-based tool for identification and annotation of proxy SNPs using HapMap
Bioinformatics, 2008 24(24):2938-2939

gs 2.0 – Generating Samples for Association Studies based on HapMap data

gs 2.0

:: DESCRIPTION

gs can be used to generate samples in testing algorithms for tag SNP selection, haplotype inference, as well as epistatic detection.

::DEVELOPER

Jing Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX

:: DOWNLOAD

 gs

:: MORE INFORMATION

Citation

Li, J and Y Chen.
Generating samples for association studies based on HapMap data.
BMC Bioinformatics 9:44, 2008.