RareVariantVis

RareVariantVis is a new software tool that facilitates the analysis and visualization of whole genome sequencing (WGS) data for germline and somatic variants in rare diseases with presumed monogenic inheritance. The tool addresses the challenges associated with analyzing and visualizing vast amounts of WGS data by providing a user-friendly interface that displays variants along their respective chromosomes.

It offers information about the exact chromosomal position, zygosity, and frequency of each variant, along with easy access to dbSNP IDs, gene associations, and variant inheritance patterns. RareVariantVis allows users to flag rare and de novo variants in different colors, enhancing the identification of potentially causative genetic variants. The tool's performance has been demonstrated using the Genome in a Bottle WGS data set.

Topic

Rare diseases;Sequencing;Genetic variation;Genomics

Detail

  • Operation: Genetic variation analysis

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 2.32.0

  • Credit: Bergen Research Foundation, Meltzer Foundation, the Research Council of Norway (Centres of Excellence funding scheme.

  • Input: -

  • Output: -

  • Contact: Tomasz Stokowy tomasz.stokowy@k2.uib.no

  • Collection: -

  • Maturity: Mature

Publications

  • RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data.
  • Stokowy T, et al. RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data. Bioinformatics 2016; 32:3018-3020. doi: 10.1093/bioinformatics/btw359
  • https://doi.org/10.1093/bioinformatics/btw359
  • PMID: 27288501
  • PMC: -

Download and documentation

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