Overlapping Mates in Small Variant Calling

DRAGEN v3.6 and later no longer treats overlapping mates as independent evidence for a given event. This improves how overlapping mates in a read pair are handled in the variant caller and accuracy. DRAGEN handles overlapping mates as follows in both the germline and somatic pipelines.

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When the two overlapping mates agree with each other on the allele with the highest HMM score, the genotyper uses the mate with the greatest difference between the highest and the second highest HMM score. The HMM score of the other mate becomes zero.

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When the two overlapping mates disagree, the genotyper sums the HMM score between the two mates, assigns the combined score to the mate that agrees with the combined result, and changes the HMM score of the other mate to zero.

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The base qualities of overlapping mates are no longer adjusted.