General filters
The General filters relate to the regions and reads in the read mappings that should be considered, and the amount of evidence the user wants to require for a variant to be called (figure 20.82):
Figure 20.82: General filters. The values shown are those that are default for Fixed Ploidy Variant detection.
Note on the use of the Low Frequency Variant Detection tool with Whole Genome Sequencing data: The default settings for the Low Frequency Variant caller are optimized for targeted resequencing protocols, and NOT whole genome sequencing (e.g. cancer gene panels) where it is not uncommon to have modest coverage for most part of the mapping, and abnormal areas (typically repeats around the centromeres) with very high coverage. Looking for low frequency variants in high coverage areas will exhaust the machine memory because there will be many low frequency variants due to some reads originating from near identical repeat sequences or simple sequencing errors.In order to run the tool on WGS data the parameter Ignore positions with coverage above should be adjusted to a lower number (typically 1000).
Subsections