Introduction to Variant Calling with Galaxy & the GVL
The 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.
At the end of this course you 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
- Run the FreeBayes variant caller to find SNVs and indels
- Visualise BAM files using the Integrative Genomics Viewer (IGV) and identify likely SNVs and indels by eye
This is a hands-on workshop and attendees should bring their own laptops.