Introduction

Identification of one or several disease causing variant(s) from the large collection of variants present in an individual is often achieved by the sequential use of heuristic filters. The recent development of whole exome sequencing enrichment designs for several non-model species created the need for a species-independent, fast and versatile analysis tool, capable of tackling a wide variety of standard and more complex inheritance models. With this aim, we developed "Mendelian", an R-package that can be used for heuristic variant filtering.The R-package Mendelian offers fast and convenient filters to analyze putative variants for both recessive and dominant models of inheritance, with variable degrees of penetrance and detectance. Analysis of trios is supported. Filtering against variant databases and annotation of variants is also included. This package is not species specific and supports parallel computation. We validated this package by reanalyzing data from a whole exome sequencing experiment on intellectual disability in humans. In a second example, we identified the mutations responsible for coat color in the dog. This is the first example of whole exome sequencing without prior mapping in the dog.We developed an R-package that enables the identification of disease-causing variants from the long list of variants called in sequencing experiments. The software and a detailed manual are available at https://github.com/BartBroeckx/Mendelian.

Publications

  1. An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors.
    Cite this
    Broeckx BJ, Coopman F, Verhoeven G, Bosmans T, Gielen I, Dingemanse W, Saunders JH, Deforce D, Van Nieuwerburgh F, 2015-01-01 - BMC bioinformatics

Credits

  1. Bart J G Broeckx
    Developer

    Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences

  2. Frank Coopman
    Developer

    Department of Applied Biosciences, Faculty of Bioscience Engineering

  3. Geert Verhoeven
    Developer

    Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine

  4. Tim Bosmans
    Developer

    Department of Medicine and Clinical Biology of Small Animals, Faculty of Veterinary Medicine

  5. Ingrid Gielen
    Developer

    Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine

  6. Walter Dingemanse
    Developer

    Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine

  7. Jimmy H Saunders
    Developer

    Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine

  8. Dieter Deforce
    Developer

    Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences

  9. Filip Van Nieuwerburgh
    Investigator

    Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences

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Summary
AccessionBT002141
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByFilip Van Nieuwerburgh