CNVphaser / CNVphaserPro 1.1 – Infer CNV Haplotypes with Variations

CNVphaser / CNVphaserPro 1.1

:: DESCRIPTION

CNVphaser infers haplotypes with variations in both copy numbers and nucleotide sequences within a CNV region

CNVphaserPro, a successor of CNVphaser and MOCSphaser to handle noisy CNV data such as microarray data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 CNVphaser / CNVphaserPro

:: MORE INFORMATION

Citation

Am J Hum Genet. 2008 Aug;83(2):157-69. doi: 10.1016/j.ajhg.2008.06.021. Epub 2008 Jul 17.
An algorithm for inferring complex haplotypes in a region of copy-number variation.
Kato M1, Nakamura Y, Tsunoda T.

ParaHaplo 4.0 beta – Tools for Haplotype-based Whole-genome Association Study using Parallel Computing

ParaHaplo 4.0 beta

:: DESCRIPTION

ParaHaplo is developing parallel computing tools for genome-wide association studies.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • OpenMPI version 1.2.5, or MPICH version 1.2.7p1

:: DOWNLOAD

 ParaHaplo

:: MORE INFORMATION

Citation

ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing.
Misawa K, Kamatani N.
Source Code Biol Med. 2011 May 24;6(1):10. doi: 10.1186/1751-0473-6-10.

MOCSphaser – Infer Haplotypes composed of Copy Numbers Alleles and SNP Alleles

MOCSphaser

:: DESCRIPTION

MOCSphaser is a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 MOCSphaser

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 15;24(14):1645-6. doi: 10.1093/bioinformatics/btn242. Epub 2008 May 20.
MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.
Kato M1, Nakamura Y, Tsunoda T.

FUGUE 0.2.3 – Haplotype Frequency Estimation

FUGUE 0.2.3

:: DESCRIPTION

FUGUE is the program used to construct haplotypes for the chromosome and linkage disequilibrium maps.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • MERLIN

:: DOWNLOAD

FUGUE

:: MORE INFORMATION

Citation:

Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR and Dunham I
A first-generation linkage disequilibrium map of human chromosome
Nature (2002) 418:544-548

Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, Camisa AL, Pazorov V, Scott KE, Carey BJ, Faith J, Katari G, Bhatti HA, Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Varde SA, Hozza MJ, Gelfand CA, Broxholme J, Abecasis GR, Boyce-Jacino MT and Cardon LR
Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots.
Nat Genet (2003) 33:382-7

MACH 1.0 – Haplotyping, Genotype Imputation & Disease Association Analysis

MACH 1.0

:: DESCRIPTION

MACH (Markov Chain Haplotyping) is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

MACH

:: MORE INFORMATION

Citation:

Li Y, Willer CJ, Ding J, Scheet P and Abecasis GR (2006)
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes.
Genet Epidemiol 34:816-834.

If you decide to use MACH, please take a minute to register.

SVEngine – Allele Specific and Haplotype Aware Structural Variants Simulator

SVEngine

:: DESCRIPTION

SVEngine (Structural Variants Engine) is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

SVEngine

:: MORE INFORMATION

Citation

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy081.
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.
Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP

SimPed – Generate Haplotype and Genotype data for Pedigree Structures

SimPed

:: DESCRIPTION

SimPed is a program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies.

::DEVELOPER

Human Genome Sequencing Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows  / Linux / MacOsX

:: DOWNLOAD

 SimPed

:: MORE INFORMATION

Citation

Leal, Yan, Muller-Myhsok (2005),
SimPed: a simulation program to generate haplotype and genotype data for pedigree structures“,
Human Heredity, 60(2):119-122.

Rehh 3.0.1 – Search for Footprints of Selection using Haplotype Homozygosity based tests

Rehh 3.0.1

:: DESCRIPTION

Rehh is an R package to search for footprints of selection using Haplotype Homozygosity based tests

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • R

:: DOWNLOAD

 Rehh

:: MORE INFORMATION

Citation

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure.
Gautier M, Vitalis R.
Bioinformatics. 2012 Apr 15;28(8):1176-7. doi: 10.1093/bioinformatics/bts115.

HaploShare 1.02 – Find Shared Haplotypes among Patients from a common recent Ancestor

HaploShare 1.02

:: DESCRIPTION

HaploShare was designed to find shared haplotypes among patients from a common recent ancestor.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICSUniversity of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 HaploShare

:: MORE INFORMATION

Citation

Genome Biol. 2015 May 9;16:92. doi: 10.1186/s13059-015-0662-9.
HaploShare: identification of extended haplotypes shared by cases and evaluation against controls.
Ying D, Sham PC, Smith DK, Zhang L, Lau YL, Yang W.

HapSeq 2 – Genotype Calling and Phasing for WGS data

HapSeq 2

:: DESCRIPTION

HapSeq2 is a program for genotyping calling and haplotype phasing from next generation sequencing data using haplotype information from jumping reads. Previously, we developed a Hidden Markov Model (HMM) based method for genotype calling and haplotype phasing from next generation data that can take into account jumping reads information across two adjacent potential polymorphic sites.

::DEVELOPER

ZhiGroup

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window/Linux

:: DOWNLOAD

 HapSeq2

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Apr 1;28(7):938-46. doi: 10.1093/bioinformatics/bts047. Epub 2012 Jan 27.
Genotype calling from next-generation sequencing data using haplotype information of reads.
Zhi D, Wu J, Liu N, Zhang K.