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Variant calling in genomics: A comparative performance analysis and decision guide

Fig 5

Change in precision from chromosome 20 to whole-genome sequencing.

Comparison of precision metrics for four variant callers (GATK, Octopus, FreeBayes, SAMtools) between the chromosome 20 subset and the whole-genome (WGS) dataset. All tools showed increase in precision on WGS data. GATK exhibited the largest improvement (from 0.662 to 0.777, ), followed closely by FreeBayes (). Octopus, which had the highest precision on chr20 (0.741), maintained the highest absolute precision on WGS (0.801) with a gain of +0.060. The precision shift suggests that a whole-genome context provides enhanced statistical power for filtering false positives. Metrics were computed with RTG Tools’ vcfeval against the Genome in a Bottle (GIAB) truth set.

Fig 5

doi: https://doi.org/10.1371/journal.pone.0339891.g005