Topic outline

  • General

    NGS - Genome variant analysis

    6-7 Feb 2018

    Bern, Hochschulstrasse 4 - Seminarraum Nr. 331/3. OG West, University of Bern

    This page is addressed to registered participants. To access course description and application form, please click here.

    This course will be taught by Walid Gharib.

    For any assistance, please contact

  • Programme


    Feb 6 - 9h15 to 17h


    • Introduction to Variant discovery
    • Fetching sequencing data using Eutilities and SRA tools
    • Indexing references & mapping/sorting/indexing alignment


    • Differences in workflows between DNA-seq (WGS, WES) and RNA-seq
    • Marking duplicates
    • Realignment around SNPs and indels

    Feb 7 - 9h15 to 17h


    • Base quality score recalibration
    • Calling the variants (single and multiple samples)
    • Joint genotyping


    • Variant filtering
    • Variant annotation
    • Installing used software for a local use
    • Optional exam
  • Prerequisites

    Participants should install "The Integrative Genome Viewer (IGV)" on their respective machines.