StarGenetics – Mendelian Genetics Cross Simulator

StarGenetics

:: DESCRIPTION

StarGenetics is a Mendelian genetics cross simulator. StarGenetics allows students to simulate mating experiments between organisms that are genetically different across a range of traits to analyze the nature of the traits in question. Its goal is to teach students about genetic experimental design and genetic concepts.

:: DEVELOPER

The STAR program at MIT

:: SCREENSHOTS

StarGenetics

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 StarGenetics

:: MORE INFORMATION

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.

MeRP 1.0 – Mendelian Randomization analysis

MeRP 1.0

:: DESCRIPTION

MeRP is a free, open-source tool designed to streamline and automate large-scale Mendelian Randomization analysis.

::DEVELOPER

Peter Yin, Benjamin F. Voight, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MeRP

:: MORE INFORMATION

Citation

MeRP: a high-throughput pipeline for Mendelian Randomization Analysis.
Yin P, Voight BF.
Bioinformatics. 2014 Nov 10. pii: btu742

GIGI-Check 1.06 – Detection of Mendelian Consistent Genotyping Errors

GIGI-Check 1.06

:: DESCRIPTION

GIGI-Check is a C++ program to detect Mendelian consistent genotyping errors of dense markers in pedigree data.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 GIGI-Check

:: MORE INFORMATION

Citation:

Cheung, CYK., Thompson, E.A., Wijsman, E.M. (2014)
Detection of Mendelian Consistent Genotyping Errors in Pedigrees.
Genetic Epidemiology 38(4):291-299

Mendelian – Heuristic Variant Filtering

Mendelian

:: DESCRIPTION

Mendelian is an R package that can be used to filter sequencing variants. It enables filtering for both dominant and recessive traits, with a wide variety of options (including reduced penetrance and detectance).

::DEVELOPER

Mendelian team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 Mendelian

:: MORE INFORMATION

Citation

An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors.
Broeckx BJ, Coopman F, Verhoeven G, Bosmans T, Gielen I, Dingemanse W, Saunders JH, Deforce D, Van Nieuwerburgh F.
BMC Bioinformatics. 2015 Nov 19;16:391. doi: 10.1186/s12859-015-0822-7.

MR-JTI v1 – Joint-tissue Transcriptome-wide Association and Mendelian Randomization analysis

MR-JTI v1

:: DESCRIPTION

MR-JTI is a joint-tissue imputation (JTI) approach and a Mendelian randomization framework for causal inference.

::DEVELOPER

Gamazon Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

MR-JTI

 :: MORE INFORMATION

Citation

Zhou D, Jiang Y, Zhong X, Cox NJ, Liu C, Gamazon ER.
A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis.
Nat Genet. 2020 Nov;52(11):1239-1246. doi: 10.1038/s41588-020-0706-2. Epub 2020 Oct 5. PMID: 33020666; PMCID: PMC7606598.