General introduction to Genome Variant Analysis (GVA14)

Overall Course Learning Objectives

• Be capable of navigating a Linux operating system and TACC's Lonestar system in particular
• Understand the biological questions, technologies, and workflows related to genome variant analysis, including:
  • Types of variants detectable by NGS
  • Terms: eQTL / GWAS / causative mutation analysis / population genetics
  • phylogenetics: evolution (e.g. quasi-species evolution), ecology (e.g. populations, pooled samples, bacterial communities)
  • Genotype / phenotype associations - either at a gross scale (e.g. mapping) or fine scale (e.g. causative mutations)
  • Technologies:
    • WGA
    • Exome
    • ddRAD
    • sequencing technologies

• Related topics which are outside the scope of this course include: allele specific expression, methylation analysis, ChIP-seq, RIP-seq

Learning Objectives: Day 1, Part 1: Linux/TACC Introduction

• Learn and practice essential Linux concepts and commands, including where to get more help & information
• Learn and practice working with TACC systems (Lonestar in particular)

Other Resources:

• Paper comparing NGS technologies (Liu et al., 2012)
• Official Illumina video | Another Illumina video
• Broad Center GA Boot Camp