Overview

Instructor: Wesley Brashear

Time: TBD

Location:

Prerequisites: Current ACCESS ID, Linux/Unix skills

This short course uses example data to complete a standard short variant discovery pipeline, from library QC and trimming, to read mapping, and calling variants using the GATK software suite.

Course Materials

• Introduction to Short Variant Discovery (Spring 2023): PDF

Agenda

This course focuses, among others, on the following topics:

• NGS library quality control (TrimGalore!, FastQC)
• Short-read reference genome alignment (bwa-mem2)
• Alignment processing and modification (SAMtools, Picard Tools)
• Variant calling (GATK)

Note: During the class sessions many aspects of the material will be illustrated live via a login to HPRC clusters. You are encouraged to contact the HPRC helpdesk with any questions regarding cluster accounts.