Overview

Instructor(s): Dr. Wesley Brashear

Time: TBD

Location:

Prerequisite(s): 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.

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Course Materials

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

Participation

During the training, attendees are expected to log in to an HPRC cluster using their own computer and complete the instructor-led examples and exercises.

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)