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.

TrioCaller 20120626 / FamLDCaller 20160215 – LD-aware Genotype Calling and Phasing program for Sequence data

TrioCaller 20120626 / FamLDCaller 20160215

:: DESCRIPTION

TrioCaller is based on a LD-aware method to infer genotypes and phasing for sequencing in trios (or mixed with undrelated individuals).

FamLDCaller is an extension of TrioCaller to handle nuclear and general family structure.

::DEVELOPER

Abecasis Group / Statistical Genetics/Genomes Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TrioCaller  / FamLDCaller

:: MORE INFORMATION

Citation

A computational method for genotype calling in family-based sequencing data.
Chang LC, Li B, Fang Z, Vrieze S, McGue M, Iacono WG, Tseng GC, Chen W.
BMC Bioinformatics. 2016 Jan 16;17(1):37. doi: 10.1186/s12859-016-0880-5.

Genome Res. 2013 Jan;23(1):142-51. doi: 10.1101/gr.142455.112. Epub 2012 Oct 11.
Genotype calling and haplotyping in parent-offspring trios.
Chen W1, Li B, Zeng Z, Sanna S, Sidore C, Busonero F, Kang HM, Li Y, Abecasis GR.

WinHAP 2.0 – Fast Haplotype Phasing program for long Genotype Sequences

WinHAP 2.0

:: DESCRIPTION

WinHAP is a fast haplotype phasing program for phasing large-scale population genotypes data. WinHAP2.0 is a significantly improved version of the WinHAP program that both process longer sequences with less computer memory usage and increases computing speed.

::DEVELOPER

Weihua Pan, Yun Xu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 WinHAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 May 30;15(1):164. [Epub ahead of print]
WinHAP2: an extremely fast haplotype phasing program for long genotype sequences.
Pan W, Zhao Y, Xu Y, Zhou F.

PLoS One. 2012;7(8):e43163. doi: 10.1371/journal.pone.0043163. Epub 2012 Aug 14.
WinHAP: an efficient haplotype phasing algorithm based on scalable sliding windows.
Xu Y1, Cheng W, Nie P, Zhou F.

hsphase – Pedigree Reconstruction, Detection of Recombination Events, Phasing and Imputation of half-sib Family Group

hsphase

:: DESCRIPTION

hsphase is an R package that implements a very fast method for phasing, sire genotype imputation, identification of paternal strand of origin and recombination events in half-sib families

::DEVELOPER

Cedric Gondro

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • R

:: DOWNLOAD

 hsphase

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jun 7;15:172. doi: 10.1186/1471-2105-15-172.
hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups.
Ferdosi MH1, Kinghorn BP, van der Werf JH, Lee SH, Gondro C.

AlphaPhase 1.1 – Phasing Genotype data

AlphaPhase 1.1

:: DESCRIPTION

AlphaPhase is a software package for phasing genotype data which uses long range phasing and haplotype library imputation methodology.

::DEVELOPER

John Hickey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ Windows

:: DOWNLOAD

 AlphaPhase

:: MORE INFORMATION

Citation

Genet Sel Evol. 2011 Mar 10;43:12. doi: 10.1186/1297-9686-43-12.
A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes.
Hickey JM1, Kinghorn BP, Tier B, Wilson JF, Dunstan N, van der Werf JH.

AlphaImpute beta – Imputing and Phasing Genotype data in Populations

AlphaImpute beta

:: DESCRIPTION

AlphaImpute is a software package for imputing and phasing genotype data in populations with pedigree information. AlphaImpute combines long range phasing with segregation analysis and haplotype library imputation (SAHLI) methodology to impute alleles and genotypes.

::DEVELOPER

John Hickey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 AlphaImpute

:: MORE INFORMATION

Citation

Genet Sel Evol. 2013 Apr 25;45:10. doi: 10.1186/1297-9686-45-10.
Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes.
Hickey JM1, Kranis A.

Hapler 1.60 – Haplotype Phasing of Population-sourced Sequence data

Hapler 1.60

:: DESCRIPTION

Hapler is a tool for assembling robust haplotype regions given alignments (from de-novo assembly or mapping to a reference) of genetically diverse sequence data. Hapler compares each sequence to every other, and groups sequences together into sets that don’t have any conflicts (minimum coloring of the sequence ‘conflict graph’). This can be done in O(n^3) time, because Hapler assumes that sequences contain no gaps (e.g., it ignores mate-pair information). Because such a minimum coloring is usually not unique, Hapler by default produces many pseudo-random colorings and only keeps haplotype groupings which are common to all. In practice this drastically increases the correctness of results.

::DEVELOPER

ND Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

  Hapler

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Apr 12;13 Suppl 2:S4. doi: 10.1186/1471-2164-13-S2-S4.
Haplotype and minimum-chimerism consensus determination using short sequence data.
O’Neil ST, Emrich SJ.

SHAPEIT 2.727 – Accurate and Efficient Phasing of Genetic datasets

SHAPEIT 2.727

:: DESCRIPTION

SHAPEIT (Segmented HAPlotype Estimation and Imputation Tool) is a program for accurate and efficient phasing of genetic datasets

::DEVELOPER

SHAPEIT Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 SHAPEIT

:: MORE INFORMATION

Citation

O. Delaneau, JF. Zagury, J. Marchini (2013)
Improved whole chromosome phasing for disease and population genetic studies.
Nature Methods  2013 Jan;10(1):5-6

mlPhaser 0.01 – Multi-Locus Haplotype Phasing

mlPhaser 0.01

:: DESCRIPTION

mlPhaser is an R package for phase haplotypes from genotypes based on a list of known haplotypes. Suited to highly diverse loci such as HLA.

::DEVELOPER

Dave Gerrard

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • R package

:: DOWNLOAD

 mlPhaser

:: MORE INFORMATION