Introduction to Variant Calling with Galaxy & the GVL
Presenter – Khalid Mahmood
This tutorial is designed to introduce the tools, datatypes and workflow of variant detection. We will align reads to the genome, look for differences between reads and reference genome sequence, and filter the detected genomic variation manually to understand the computational basis of variant calling.
In this tutorial we cover the concepts of detecting small variants (SNVs and indels) in human genomic DNA using a small set of reads from chromosome 22.
By the end of this training, participants will be able to:
- work with the FASTQ format and base quality scores
- align reads to generate a BAM file and subsequently generate a pileup file
- call simple variants (SNVs and indels) using a variant caller
- visualise BAM files using the Integrative Genomics Viewer (IGV) and identify likely SNVs and indels by eye.
Prerequisites and Requirements
This workshop requires does not require any previous experience but familiarity with Galaxy or completion of “Introduction to Galaxy” workshop is recommended.
This is a hands-on workshop and attendees must bring their own laptops to the workshop with the following software preinstalled:
- access to Uniwireless/Eduroam
- web browser (Firefox or Chrome recommended)
- IGV (Integrated Genome Viewer).