Modeling of Correlated Errors Across Reads

DRAGEN has two algorithms that model correlated errors across reads in a given pileup.

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Foreign read detection (FRD) detects mismapped reads. FRD modifies the probability calculation to account for the possibility that a subset of the reads were mismapped. Instead of assuming that mapping errors occur independently per read, it estimates the probability that a burst of reads is mismapped, incorporating such evidence as MAPQ and skewed AF. For more information, see Foreign Read Detection.

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The base quality drop off (BQD) algorithm detects correlated base call errors using a mechanism that detects systematic and correlated base call errors caused by the sequencing instrument. The detection mechanism exploits certain properties of those errors (strand bias, position of the error in the read, base quality) to estimate the probability that the alleles are the result of a systematic error event rather than a true variant. For more information, see Base Quality Dropoff.