trioPhaser – Using Mendelian inheritance logic to improve Genomic Phasing of Trios

trioPhaser

:: DESCRIPTION

trioPhaser is a containerized software tool that uses both Mendelian inheritance logic and SHAPEIT4 to phase trios when gVCF files are available.

::DEVELOPER

trioPhaser team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Docker
  • Python

:: DOWNLOAD

trioPhaser

:: MORE INFORMATION

Citation

Miller DB, Piccolo SR.
trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios.
BMC Bioinformatics. 2021 Nov 22;22(1):559. doi: 10.1186/s12859-021-04470-4. PMID: 34809557; PMCID: PMC8607709.

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.

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 / Chen 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.

SHAPEIT 4.2.1 – Accurate and Efficient Phasing of Genetic datasets

SHAPEIT 4.2.1

:: DESCRIPTION

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

::DEVELOPER

Jonathan Marchini

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 SHAPEIT

:: MORE INFORMATION

Citation

Delaneau O, Zagury JF, Robinson MR, Marchini JL, Dermitzakis ET.
Accurate, scalable and integrative haplotype estimation.
Nat Commun. 2019 Nov 28;10(1):5436. doi: 10.1038/s41467-019-13225-y. PMID: 31780650; PMCID: PMC6882857.

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

AlphaPlantImpute – Phasing and Imputing Genotype data in Plant Breeding Populations

AlphaPlantImpute

:: DESCRIPTION

AlphaPlantImpute is a software package designed for phasing and imputing genotype data in plant breeding populations. AlphaPlantImpute can be implemented within and across bi-parental populations to phase and impute focal individuals genotyped at low-density to high-density. Focal individuals can be descendants of a bi-parental cross at various levels of selfing or can be parents of one or more bi-parental populations. All information on the model of analysis, input files and their layout, is specified in a single parameter file.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

AlphaPlantImpute

:: MORE INFORMATION

Citation

Gonen S, Wimmer V, Gaynor RC, Byrne E, Gorjanc G, Hickey JM.
A heuristic method for fast and accurate phasing and imputation of single-nucleotide polymorphism data in bi-parental plant populations.
Theor Appl Genet. 2018 Nov;131(11):2345-2357. doi: 10.1007/s00122-018-3156-9. Epub 2018 Aug 4. PMID: 30078163; PMCID: PMC6208939.

AlphaPeel 0.1.0 – Calling, Phasing, and Imputing Genotype and Sequence data in Pedigree Populations

AlphaPeel 0.1.0

:: DESCRIPTION

AlphaPeel is a software package for calling, phasing, and imputing genotype and sequence data in pedigree populations. This program implements single locus peeling, multi locus peeling, and hybrid peeling.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

AlphaPeel

:: MORE INFORMATION

Citation

Whalen A, Ros-Freixedes R, Wilson DL, Gorjanc G, Hickey JM.
Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees.
Genet Sel Evol. 2018 Dec 18;50(1):67. doi: 10.1186/s12711-018-0438-2. PMID: 30563452; PMCID: PMC6299538.

AlphaPhase 1.2 – Phasing Genotype data

AlphaPhase 1.2

:: DESCRIPTION

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

::DEVELOPER

AlphaGenes

:: 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 1.9.8.3 – Imputing and Phasing Genotype data in Populations

AlphaImpute 1.9.8.3

:: 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

AlphaGenes

:: 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.

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.