Quality filters

Figure 22.80 gives an example of a variant called when the base quality filter is NOT applied, and not called when it is. When switching on the 'Show quality scores' option in the side panel of the reads it becomes visible that the reads that carry the potential 'G' variant tend to have poor quality. Note that the error in the example shown is a 'typical' Illumina error: the reference has a 'T' that is surrounded by stretches of 'G', the 'G' signals 'drowning' the signal of the 'T'. As all reads that have a base with quality less than 20 in this potential variant position are ignored when the 'Base quality filter' is turned on, no variant is called, most likely because it now does not meet the requirements of either the 'Minimum coverage', 'Minimum count' or 'Minimum frequency' filters.

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Figure 22.80: Example of a variant called when the base quality filter is NOT applied, and not called when it is.