Intro to Somatic WGS and Exome Variant Analysis
- Somatic variation, variant types (SNVs, small indels, CNVs, SVs, LOH), VCFs, variant allele fraction (VAF), purity estimation and tumor clonality.
- Compare and contrast the merits of exome and WGS data for variant calling
- Compare germline and somatic variant calling strategies
- Consider the features of major variant types detected in NGS data
- Perform somatic variant calling of various types using tools specific to each type
- Understand the basic features of the VCF format
- Merge multiple VCFs into a single combined VCF
- Perform variant filtering to identify a high quality set of variants
- Annotate variants with respect to transcript annotations, population frequency, predicted function, etc.
- Manually review variants of each type to better understand how variant callers use read alignment data to identify variants