Lecture
- Introduction to somatic variants
- Framework for short variant discovery (GATK)
- Variant callers
- Variant filtering and annotation
- IGV for visualization and validation
- Common somatic mutational analyses
Practical
- The GATK pipeline of somatic short variant discovery
- Examining variants in IGV
- Introduction to maftools
- Visualization and analysis with maftools
The lecture in this session will introduce you to different types of somatic mutations, focusing on short variants (single nucleotide variants and insertions/deletions), the GATK best practices framework to short variant discovery, and common challenges for accurate somatic mutation detection. We will also introduce common variant calling methods and variant callers, followed by a summary of variant filtering and annotation steps. A few examples of how IGV could be used to validate and visualize somatic variants will also be included. Finally, we will discuss downstream analyses commonly performed in cancer genomics studies.
In the practical session, you will gain hands-on experience of running through the GATK pipeline for somatic mutation discovery as well as annotating variants. You will also have a chance to use IGV to examine high-confidence variants versus probable sequencing artifacts.