Changes

This page outlines a generic plan for analysis of a whole exome sequencing project. The idea is that the points listed here might serve as a starting point for discussion of the analyses needed in a specific project.

This page outlines a generic plan for analysis of a whole exome sequencing project. The idea is that the points listed here might serve as a starting point for discussion of the analyses needed in a specific project.

== Read Mapping and Variant Calling ==

= Read Mapping and Variant Calling =

The first step in any analysis is to map sequence reads, callibrate base qualities, and call variants. Even at this stage, some simple quality metrics can be evaluated and will help identify potentially problematic samples.

The first step in any analysis is to map sequence reads, callibrate base qualities, and call variants. Even at this stage, some simple quality metrics can be evaluated and will help identify potentially problematic samples.