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.

plotIBD 20111108 – Plotting Sampled Inheritance Vectors in Pedigrees

plotIBD 20111108

:: DESCRIPTION

plotIBD is a perl script to assist with plotting sampled inheritance vectors in pedigrees

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 plotIBD

:: MORE INFORMATION

Citation:

Hum Hered. 2011;72(4):289-97. doi: 10.1159/000334083. Epub 2011 Dec 23.
Estimation and visualization of identity-by-descent within pedigrees simplifies interpretation of complex trait analysis.
Marchani EE1, Wijsman EM.

GIGI 1.06.1 – Genotype Imputation Given Inheritance

GIGI 1.06.1

:: DESCRIPTION

GIGI is a computer program to impute missing genotypes on pedigrees.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GIGI

:: MORE INFORMATION

Citation:

Cheung, CYK., Thompson, E.A., Wijsman, E.M. (2013).
GIGI: An approach to effective imputation of dense genotypes on large pedigrees.
American Journal of Human Genetics 92:504-516

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