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A introduction to SNV analyses in whole genome sequencing

Instructors

About this workshop

In this 2-hour workshop, you will have hands-on experience on SNV calling and analysis. You will be provided toy short-read sequencing samples, followed by read alignments, variant calling and pathogenicity analysis.

Accesing the workshop

  • Docker image: link
  • Workshop material: link

Overview

This workshop will guide you through the workflow of a simple genomic SNV analysis.

This is a hands-on workshop, which means you will be given time to get the tools running.

For each task, you will be given a brief instruction prior to getting your hands dirty. At the end of the given time, there will be a brief summary.

Pre-requisites

Basic knowledge of using command line and Rstudio is ideal. Although strictly speaking, no prior knowledge is required to attend this workshop.

Participation

The workshop runs for 2 hours. You will find tasks and related information in the worksheet.

If you run into any problems, please describe the issue and send via zoom chat. The instructors will be monitoring the chat panel and answer any question in real time.

Tools to be used

Time outline

For this 120-minute workshop:

Activity Time
Introduction 5m
Working Environment: command line and Rstudio 15m
Read Alignment: bwa and samtools 20m
SNV calling: Strelka2 20m
Pathogenicity analysis 50m
Summary 10m

Workshop goals and objectives

Variant calling is a vital component of genomics studies. Genomic variants have been found in various structures and sizes, including single-nucleotide variants (SNVs), small insertion and deletions (INDELs), copy number variants (CNVs) and structural variants (SVs). Computational tools for detecting these variants are developed with different underlying approaches.

This workshop is designed to offer a hands-on experience on genomic variant calling and analysis. The tasks are designed to guide you through the key steps of SNV analysis on a tumour/normal paired sample.

Learning goals

  • To understand the general workflow of a genomic variant analysis
  • To identify methods to handle short-read sequencing data and variant calls

Learning objectives

  • To recall the key concepts in genomic variant analysis
  • To apply the concepts in SNV calling to germline and paired tumour/normal data
  • To perform SNV analysis using publicly available resources

About

WEHI Masterclass Day 3: Genomics

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MIT
LICENSE.md

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