Introduction

The search for causative genetic variants in rare diseases of presumed monogenic inheritance has been boosted by the implementation of whole exome (WES) and whole genome (WGS) sequencing. In many cases, WGS seems to be superior to WES, but the analysis and visualization of the vast amounts of data is demanding.To aid this challenge, we have developed a new tool-RareVariantVis-for analysis of genome sequence data (including non-coding regions) for both germ line and somatic variants. It visualizes variants along their respective chromosomes, providing information about exact chromosomal position, zygosity and frequency, with point-and-click information regarding dbSNP IDs, gene association and variant inheritance. Rare variants as well as de novo variants can be flagged in different colors. We show the performance of the RareVariantVis tool in the Genome in a Bottle WGS data set.https://www.bioconductor.org/packages/3.3/bioc/html/RareVariantVis.htmltomasz.stokowy@k2.uib.noSupplementary data are available at Bioinformatics online.

Publications

  1. RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data.
    Cite this
    Stokowy T, Garbulowski M, Fiskerstrand T, Holdhus R, Labun K, Sztromwasser P, Gilissen C, Hoischen A, Houge G, Petersen K, Jonassen I, Steen VM, 2016-10-01 - Bioinformatics (Oxford, England)

Credits

  1. Tomasz Stokowy
    Developer

    Department of Clinical Science, University of Bergen, Norway

  2. Mateusz Garbulowski
    Developer

    Department of Informatics, Silesian University of Technology, Poland

  3. Torunn Fiskerstrand
    Developer

    Department of Clinical Science, University of Bergen, Norway

  4. Rita Holdhus
    Developer

    Department of Clinical Science, University of Bergen, Norway

  5. Kornel Labun
    Developer

    Department of Informatics, Computational Biology Unit, Norway

  6. Pawel Sztromwasser
    Developer

    Department of Clinical Science, University of Bergen, Norway

  7. Christian Gilissen
    Developer

    Department of Human Genetics, Radboud University Medical Center

  8. Alexander Hoischen
    Developer

    Department of Human Genetics, Radboud University Medical Center

  9. Gunnar Houge
    Developer

    Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Norway

  10. Kjell Petersen
    Developer

    Department of Informatics, Computational Biology Unit, Norway

  11. Inge Jonassen
    Developer

    Department of Informatics, Computational Biology Unit, Norway

  12. Vidar M Steen
    Investigator

    Department of Clinical Science, University of Bergen, Norway

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT000811
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionNorway
Submitted ByVidar M Steen