Basic Variant Detection
The Basic Variant Detection tool does not rely on any assumptions on the data, and does not estimate any error model. It can be used on any type of sample. It will call a variant if it satisfies the requirements that you specify when you set the filters (see Filters). The tool has a single parameter (figure 29.7) that is specific to this tool: the user is asked to specify the 'ploidy' of the sample that is being analyzed. The value of this parameter does not have an impact on which variants are called - it will merely determine the contents of the 'hyper-allelic' column that is added to the variant track table: variants that occur in positions with more variants than expected given the specified ploidy, will have 'Yes' in this column, other variants will have 'No' (see Variant Detectors - the outputs for a description of the outputs).
Figure 29.7: The Basic Variant Detection parameters.