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  General

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  NGS - Genome variant analysis

  30-31 May 2017

  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.
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  Programme

  Schedule

  May 30- 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

  May 31- 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
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  Material

  Course website (all materials included)