Significance of variant

At a given position, when the reads have been filtered, the remaining reads will be compared to the reference sequence to see if they are different at this position (for de novo assembly the consensus sequence is used for comparison). For a variant to be reported, it has to comply with the significance threshold specified in the dialog shown in figure 33.5.

Image SNP_detection_step3
Figure 33.5: Significance thresholds.

Below, there is an Advanced option letting you specify additional requirements. These will only take effect if the Advanced checkbox is checked.

When there are ambiguity bases in the reads, they will be treated as separate variants. This means that e.g. a Y will not be collapsed with C or T in other reads. Rather, the Ys will be counted separately.

Variant filters

Below the significance settings, there are filters that can be useful for removing false positives: