SeqMan Pro provides the option to use a neighborhood quality score threshold when identifying variants. This threshold can be changed by opening SeqMan Pro’s Variant Discovery Parameters dialog and defining a new ‘Neighborhood Window’ value. By default, the Neighborhood Window value is zero, meaning that the neighborhood quality score threshold is not used.
A neighborhood quality score is equal to the lowest quality score of any of the bases in the defined window surrounding a variant base. The size of the window can be adjusted by editing the Neighborhood Window value. For example, if the Neighborhood Window value is set to 5, then the 5 bases upstream and the 5 bases downstream from the variant base will be considered. If the specified window contains one or more mismatches to the reference sequence, the putative variant will be rejected.
Unless you have specific thresholds you would like to use, you may wish to start with the Q-Score Threshold values from Altshuler et al. (2000):
•Minimum Score at SNP: 20
•Minimum Neighborhood Score: 15
•Neighborhood Window: 5