Fig. 5: The performance of different filtering methods when applied to coding or non-coding variants.
From: FVC as an adaptive and accurate method for filtering variants from popular NGS analysis pipelines
The coding and non-coding variant calls used as testing data are derived from whole-genome sequencing data (HG001, HG003, HG004, and HG006) at 30× coverage and identified by GATK, Varscan2, Mutect2, and DeepVariant, separately. The different filtering methods are separately assessed on the a coding variants using MCC; b coding variants measured using OFO; c non-coding variants measured using MCC; and d non-coding variants using OFO. FVC achieves the highest MCC and the lowest log OFO when applied to both types of variants identified by GATK HaplotypeCaller, Varscan2, Mutect2, and DeepVariant. The circle indicates the metric score achieved by the filtering method when applied to each specified testing data. The error bar indicates the 95% confidence intervals (n = 4 biologically independent samples). Asterisk denotes the significance of the comparison using a one-sided paired T-test (*p < 0.05, **p < 0.001), where the null hypothesis is that the FVC performs no better than the compared method.
