NGS - Genome variant analysis - Feb 2018
Section outline
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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.
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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
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Participants should install "The Integrative Genome Viewer (IGV)" on their respective machines.