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 training@sib.swiss.

  • Programme

    Schedule

    Feb 6 - 9h15 to 17h

    Morning

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

    Afternoon

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

    Feb 7 - 9h15 to 17h

    Morning

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

    Afternoon

    • 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.