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 31.8):

Image generalfilters
Figure 31.8: 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 Detection tool 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).

Reference masking

The 'Reference masking' filters allow the user to only perform variant calling (including error model estimation) in specific regions. In addition to selecting an annotation track, there are two parameters to specify:

Read filters

The Read filters determine which reads (or regions) should be considered when calling the variants.

Coverage and count filters

These filters specify absolute requirements for the variants to be called. Note that suitable values for these filters are highly dependent on the coverage in the sample being analyzed: These values are calculated for each of the detected candidate variants. If the candidate variant meets the specified requirements, it is called. Note that when the values are calculated, only the 'countable reads' - the reads chosen by the user to NOT be ignored - are considered. For example, if the user had specified to ignore reads from broken pairs, they will not be countable. This is also the case for non-specific reads, and for reads with bases at the variant position that does not fulfill the base quality requirements specified by the 'Base Quality Filter' (see the section on 'Noise filters' below). Also note that overlapping paired reads only count as one read since they only represent one fragment.