Tag: Haplotype

harp 20140925 – Haplotype Analysis of Reads in Pools

harp 20140925

:: DESCRIPTION

harp : Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. harp implements an EM algorithm to calculate the frequencies of known haplotypes from pooled sequence data.

::DEVELOPER

Novembre Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 harp

 :: MORE INFORMATION

Citation

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data
Darren Kessner; Tom Turner; John Novembre
Mol Biol Evol (2013) 30 (5): 1145-1158. doi: 10.1093/molbev/mst016

hapQTL 0.99 – Haplotype Quantitative Loci

hapQTL 0.99

:: DESCRIPTION

hapQTL performs association testing between local haplotypes and phenotypes at each core marker.

::DEVELOPER

Yongtao Guan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

 hapQTL

:: MORE INFORMATION

Citation

Genetics. 2014 Jul;197(3):823-38. doi: 10.1534/genetics.114.164814. Epub 2014 May 8.
Detecting local haplotype sharing and haplotype association.
Xu H, Guan Y

gTDT 0.01 – A group-wise TDT for Haplotype-based Association Testing of Rare Variants with complex Disease

gTDT 0.01

:: DESCRIPTION

gTDT implemented gene-based or group-wise TDT for rare variant aggregation analysis. Currently gTDT implemented haplotype-based tests for 6 models, M1-M6. It takes as input a ped file and a dat file that specify the relationships, and a VCF file that stores genotype data.

::DEVELOPER

gTDT team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 gTDT 

:: MORE INFORMATION

Citation

A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis.
Chen R, Wei Q, Zhan X, Zhong X, Sutcliffe J, Cox N, Cook EH, Li C, Chen W, Li B.
Bioinformatics. 2015 Jan 6. pii: btu860.

PEDIBD – Pedigree IBD & Haplotype Inference

PEDIBD

:: DESCRIPTION

PEDIBD infers pairwise Infer identical-by-descent (IBD) and skips haplotype and inheritance construction

::DEVELOPER

Xin Li 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MatLab

:: DOWNLOAD

  PEDIBD

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Nov;18(11):1411-21. doi: 10.1089/cmb.2011.0167. Epub 2011 Sep 16.
Haplotype reconstruction in large pedigrees with untyped individuals through IBD inference.
Li X1, Li J.

XQTL 1.0 – Gamily-based Allelic / Haplotype Association Test

XQTL 1.0

:: DESCRIPTION

XQTL is a family-based allelic/haplotype association test for quantitative traits using X-linked SNP/two-locus markers in a nuclear family design. XQTL adopts the framework of the orthogonal model implemented in the QTDT program with modification of the sex-specific score for X-linked genotypes. XQTL also takes into account the dosage effect due to female X chromosome inactivation.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Unix/Windows

:: DOWNLOAD

 XQTL

:: MORE INFORMATION

Citation

Zhang L, Martin ER, Morris RW, Li YJ. (2009)
Association test for X-linked QTL in family-base d designs.
American Journal of Human Genetics

Chaplin 1.2.3 – Case-control Haplotype Inference package

Chaplin 1.2.3

:: DESCRIPTION

Chaplin (Case-control haplotype inference package.) is a software program for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study.

::DEVELOPER

Epstein software

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

   Chaplin

:: MORE INFORMATION

Citation

Epstein MP and Satten GA (2003).
Inference on haplotype effects in case-control studies using unphased genotype data.
Am. J. Hum. Genet. 73:1316-1329

Satten GA and Epstein MP (2004).
Comparison of prospective and retrospective methods for haplotype inference in case-control studies.
Genet Epidemiol. 2004 Nov; 27(3):192-201

HAPLO-IHP – Haplotype Inference using Identified Haplotype Patterns

HAPLO-IHP

:: DESCRIPTION

HaploIHP is a program for haplotype reconstruction using identified haplotypes and haplotype patterns

::DEVELOPER

Kui Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Perl

:: DOWNLOAD

 HaploIHP

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Sep 15;23(18):2399-406. Epub 2007 Jul 21.
Haplotype inference for present-absent genotype data using previously identified haplotypes and haplotype patterns.
Yoo YJ1, Tang J, Kaslow RA, Zhang K.

FINDHAP V4 – Find Haplotypes and Impute Genotypes

FINDHAP V4

:: DESCRIPTION

FINDHAP is a program to find haplotypes and impute genotypes from multiple marker sets and sequence data

::DEVELOPER

Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Fortran

:: DOWNLOAD

  FINDHAP

:: MORE INFORMATION

Citation

J Dairy Sci. 2013 Jan;96(1):668-78. doi: 10.3168/jds.2012-5702. Epub 2012 Oct 11.
Genomic imputation and evaluation using high-density Holstein genotypes.
VanRaden PM1, Null DJ, Sargolzaei M, Wiggans GR, Tooker ME, Cole JB, Sonstegard TS, Connor EE, Winters M, van Kaam JB, Valentini A, Van Doormaal BJ, Faust MA, Doak GA.

Haplo Stats 1.8.6 – Statistical Methods for Haplotypes When Linkage Phase is Ambiguous

Haplo Stats 1.8.6

:: DESCRIPTION

Haplo Stats is a suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers), while also allowing for missing alleles.

::DEVELOPER

Division of Biomedical Statistics and Informatics,  Mayo Clinic

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Haplo Stats

:: MORE INFORMATION

Citation

Am J Hum Genet. 2002 Feb;70(2):425-34. Epub 2001 Dec 27.
Score tests for association between traits and haplotypes when linkage phase is ambiguous.
Schaid DJ1, Rowland CM, Tines DE, Jacobson RM, Poland GA.

WhatsHap – Haplotype Assembly for Future-Generation Sequencing Reads

WhatsHap

:: DESCRIPTION

WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads.

::DEVELOPER

The Algorithms for Computational Genomics group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • C++

:: DOWNLOAD

 WhatsHap

:: MORE INFORMATION

Citation

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A.
J Comput Biol. 2015 Jun;22(6):498-509. doi: 10.1089/cmb.2014.0157