Fig. 4: Example of partially called complex variant counted as both false positives and false negatives.
From: A diploid assembly-based benchmark for variants in the major histocompatibility complex
The CCS-DeepVariant VCF from PacBio HiFi reads incorrectly filters the 2-bp deletion and 9 of the 13 SNVs in the region (filtered variants are light gray boxes). The benchmark correctly calls this complex variant, and represents it as a 26-bp insertion of a TG tandem repeat followed by a 29-bp deletion of adjacent tandem repeats. When comparing this VCF to our MHC benchmark, the benchmark insertion and deletion variants are counted as false negatives, while the 5 SNVs called are counter-intuitively counted as false positives because the other variants are incorrectly filtered. If the CCS-DeepVariant VCF had not filtered all of the other variants, all variants would be counted as true positives.
