Course: STRUCTURAL VARIANT DETECTION AND COMPARISON
Dates: 11-13 December 2023 | Online
Course website: https://www.physalia-courses.org/courses-workshops/svs/
We are delighted to invite you to the upcoming Biostars course on "Structural Variant Detection and Comparison." This exciting course aims to introduce biologists and bioinformaticians to the fascinating field of Structural Variant (SV) detection and comparison. Held online to foster international participation, this course will equip you with valuable insights and practical skills in identifying and comparing germline and somatic structural variations.
Course Overview:
Structural Variants, genomic alterations larger than 50bp, have significant implications for multiple diseases and phenotypes. In this three-day course, we will explore various software and analysis workflows, encompassing short to long read approaches using assembly or mapping-based methods to identify these variants. Learn how to filter and assess SV and obtain a trio/population level VCF file by comparing SV. Lastly, discover how to evaluate their functional impact and prioritize and QC these variants.
Course Format:
The course will be structured in modules over three days. Each day will commence with an introductory lecture, followed by interactive class discussions of key concepts. The majority of each day will be dedicated to hands-on practical sessions. You will have the opportunity to work with the instructor to demonstrate specific skills and apply them independently to complete individual exercises. After each exercise, we will collectively discuss the interpretation of results.
Target Audience & Assumed Background:
Whether you are a beginner or an experienced researcher, this course is tailored for individuals interested in comparing genomes and understanding genomic similarities and variations. We will start by introducing general concepts of comparative genomics, progressing to cover major analysis steps from raw sequencing data to assessing variations' impact on the phenotype.
A background in biology is recommended for attendees. Some familiarity with genomic data and formats arising from NGS sequencing experiments is also desirable. As we will utilize command-line Linux in the hands-on practical exercises, we will dedicate one session to introduce basic and advanced Linux concepts for data processing on the Amazon cloud (AWS).
Learning Outcomes:
By the end of the course, participants will have gained expertise in the following areas:
- Identifying Structural Variants using mapping or assembly approaches
- Detecting Structural Variants from long and short read data
- Comparing and filtering Structural Variants
- Annotating Structural Variants (gene overlap, population frequency)
- Generating a trio/population VCF file for Structural Variants
- Identifying mosaic/somatic Structural Variants
Example Data & Bring Your Own Data:
Throughout the course, we will utilize data from a human genome sequences project for the example analyses. Additionally, we encourage participants to bring, analyze (if possible), and discuss their own data, enhancing the relevance and practicality of the training.
Course Schedule:
- Monday: General introduction, genome assembly strategies, and reference mapping
- Tuesday: Variant calling for short and long reads
- Wednesday: In-depth variant calling for long reads and variant calling annotation
Time: 2-8 pm Berlin time each day
