Base Quality Dropoff

Conventional variant callers treat sequencing errors as independent across reads, however bursts of errors can occur at a specific locus and increase the number of false positives.

These errors have distinct characteristics differentiating them from true variants. The base quality drop off (BQD) algorithm is a detection mechanism that exploits certain properties of those errors (strand bias, position of the error in the read, low mean base quality over said subset of reads at the locus of interest) and incorporates them into the probability calculation.