Introduction to NGS analysis

• Overview
• Running an interactive job on Raven
• Setup simulated reads
• Quality Control
• Mapping reads
  • Mapping reads using bowtie
  • Mapping reads using bwa
• Variant discovery
  • Variant discovery on bwa data using GATK
  • Variant discovery on bowtie data using GATK
• Comparisons between workflows
• Summary of file formats