Section outline

  • 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