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.

GINDEL 201601 – Deletion and Insertion Genotype Calling

GINDEL 201601

:: DESCRIPTION

GINDEL is an approach for calling genotypes of both insertions and deletions from sequence reads.

::DEVELOPER

GINDEL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GINDEL

:: MORE INFORMATION

Citation:

PLoS One. 2014 Nov 25;9(11):e113324. doi: 10.1371/journal.pone.0113324. eCollection 2014.
GINDEL: accurate genotype calling of insertions and deletions from low coverage population sequence reads.
Chu C, Zhang J, Wu Y

crlmm 1.42.0 – Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

crlmm 1.42.0

:: DESCRIPTION

The R package crlmm implements a multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number.

::DEVELOPER

Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 crlmm

:: MORE INFORMATION

Citation

J Stat Softw. 2011 May 1;40(12):1-32.
Using the R Package crlmm for Genotyping and Copy Number Estimation.
Scharpf RB1, Irizarry RA, Ritchie ME, Carvalho B, Ruczinski I.

ALCHEMY 1.07 – An automated, Population Genetic model driven SNP Genotype Calling method

ALCHEMY 1.07

:: DESCRIPTION

ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods.

::DEVELOPER

ALCHEMY team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 ALCHEMY 

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Dec 1;26(23):2952-60. doi: 10.1093/bioinformatics/btq533. Epub 2010 Oct 5.
ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations.
Wright MH1, Tung CW, Zhao K, Reynolds A, McCouch SR, Bustamante CD.

optiCall 0.7.0 – Robust Genotype-calling Algorithm

optiCall 0.7.0

:: DESCRIPTION

optiCall is a robust genotype-calling algorithm for calling rare, low-frequency and common variants from SNP microarray intensity data.

::DEVELOPER

Tejas Shah & Carl Anderson (opticall@sanger.ac.uk.)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 optiCall

:: MORE INFORMATION

Citation

T. S. Shah, J. Z. Liu, J. A. B. Floyd, J. A. Morris, N. Wirth, J. C. Barrett and C. A. Anderson
optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants
Bioinformatics (2012) 28 (12): 1598-1603.

iCall – Genotype-calling algorithm for rare and common Variants on the Illumina Exome Array.

iCall

:: DESCRIPTION

iCall is an improved genotype-calling algorithm for rare and common variants on the Illumina exome array. The algorithm does not rely on having prior training data and it can asssign genotypes to hybridization data from thousands of individuals simultaneously.

::DEVELOPER

StatGen , Singapore

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 iCall

 :: MORE INFORMATION

Citation

iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array.
Zhou J, Tantoso E, Wong LP, Ong RT, Bei JX, Li Y, Liu J, Khor CC, Teo YY.
Bioinformatics. 2014 Mar 12.

Illuminus – Genotype Calling algorithm

Illuminus

:: DESCRIPTION

Illuminus is a program that calls genotype from the Illumina BeadArray platform which does not rely on having prior training data or require computationally intensive procedures. The algorithm can assign genotypes to hybridization data from thousands of individuals simultaneously and pools information across multiple individuals to improve the calling. The method can accommodate variations in hybridization intensities which result in dramatic shifts of the position of the genotype clouds by identifying the optimal coordinates to initialize the algorithm.

::DEVELOPER

StatGen , Singapore

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 Illuminus

:: MORE INFORMATION

Citation

Teo YY, Inouye M, Small KS, Gwilliam R, Deloukas P, Kwiatkowski DP and Clark TG. (2007)
A genotype calling algorithm for the Illumina BeadArray platform.
Bioinformatics (Oxford, England), 23(20), 2741-2746

fitTetra 1.0 – Genotype Calling of Tetraploid Samples based on bi-allelic Marker Assays

fitTetra 1.0

:: DESCRIPTION

fitTetra is an R package for genotype calling of tetraploid samples based on bi-allelic marker assays such as Illumina GoldenGate, Infinium and KASPar. The main characteristic of such assays is that they produce two signals for a sample for a given marker, one signal for each of the two alleles.

::DEVELOPER

Wageningen UR Plant Breeding

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 fitTetra

:: MORE INFORMATION

Citation:

Voorrips RE, Gort G, Vosman B (2011)
Genotype calling in tetraploid species from bi-allelic marker data using mixture models.
BMC Bioinformatics 2011, 12:172;

DBM – Dynamic Bayesian Markov model for Genotype Calling

DBM

:: DESCRIPTION

DBM is a Dynamic Bayesian Markov model for genotype calling, haplotype inference, de novo inference of population structure and local admixture for next-gen sequencing data.

::DEVELOPER

Yu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DBM

:: MORE INFORMATION

Citation

A dynamic Bayesian Markov model for phasing and characterizing haplotypes in next-generation sequencing.
Zhang Y.
Bioinformatics (2013) 29 (7): 878-885.