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DNA Variant Analysis with R Bioconductor

Workshop Overview

In this workshop, we will use R to analyze DNA variants from Variant Call Format files to identify those likely to have a functional impact. It is intended for those with intermediate R programming skills.

Learning Objectives

  •   Examine the header and metadata of a Variant Call Format (VCF) file  
  •   Select variants in genes of interest  
  •   Get transcripts and genotypes for selected variants  
  •   Locate regions of genes where variants fall (exons, introns, etc.)  
  •   Get the predicted impact of variants  
  •   Export variants to a Browser Extensible Data (BED) file and view in UCSC browser
  •   Perform pathway analysis on variants of interest


You must have some R programming experience to benefit from this course. Please feel free to contact the instructor if you have questions about this.


Please have the latest versions of R and R Bioconductor installed, as well as RStudio, installed on your laptop prior to the workshop.


Karla Lindquist, PhD is the Scientific Lead of the UCSF Library Data Science Initiative.

Related LibGuide: Bioinformatics and Statistics Resources by Karla Lindquist

Tuesday, June 4, 2019
2:00pm - 5:00pm
Mission Bay
  Bioinformatics and Statistics     Data Science Initiative     Programming  
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Event Organizer

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Karla Lindquist