ACES: Introduction To Short Variant Discovery


Instructor: Wesley Brashear

Time: Tuesday, November 7, 2023 — 10:00AM-12:30PM CT

Location: online using Zoom

Prerequisites: Current ACCESS ID, Unix/Linux 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


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.