Targeted sequencing, also known as "targeted resequencing" or "amplicon sequencing" is a focused approach to genome sequencing with only selected areas of the genome being sequenced. In cancer research and diagnostics, targeted sequencing is usually based on sequencing panels that target a number of known cancer-associated genes.
Thirteen ready-to-use workflows are available for analysis of targeted amplicon sequencing data (figure 20.1). The concept of the pre-installed ready-to-use workflows is that read data are used as input in one end of the workflow, and after running it, the workflow will output a Track List and a table with all the identified variants, which may or may not have been subjected to different kinds of filtering and/or annotation.
In this chapter we will discuss what the individual ready-to-use workflows can be used for and go through step by step how to run the workflows.
Remember you will have to prepare data with the Prepare Raw Data workflow described in Preparing Raw Data before you proceed to running any of these workflows.