Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking

Table 2 Performance of variant callers in tumor-normal paired mode and tumor-only mode, when run with their parameter default values, without the limit of detection, or with the tuned parameter values, on samples containing only SNVs

Parameter values	Variant calling mode	Dataset	VarDict		Mutect2		LoFreq		VarScan2		FreeBayes		Strelka2
Parameter values	Variant calling mode	Dataset	TPR	PPV	TPR	PPV	TPR	PPV	TPR	PPV	TPR	PPV	TPR	PPV
Default	Tumor-normal paired	Whole cohort	0.684	0.984	0.373	0.981	0.220	0.982	N.A.	N.A.	N.A.	N.A.	0.700	0.913
Default	Tumor-only	Whole cohort	0.685	0.763	0.643	0.754	0.796	0.790	N.A.	N.A.	N.A.	N.A.	N.A.	N.A.
No detection limit	Tumor-normal paired	Whole cohort	0.833	0.986	0.373	0.981	N.A.	N.A.	0.195	0.979	0.682	0.770	N.A.	N.A.
No detection limit	Tumor-only	Whole cohort	0.835	0.797	0.643	0.754	N.A.	N.A.	0.884	0.010	0.682	0.770	N.A.	N.A.
Tuned	Tumor-normal paired	Training set	0.862	0.955	0.738	0.984	0.240	0.982	0.323	1.0	N.A.	N.A.	0.720	0.935
	Tumor-normal paired	Test set	0.862	0.955	0.741	0.986	0.258	0.987	0.117	1.0	N.A.	N.A.	N.A.	N.A.
	Tumor-only	Training set	0.835	0.797	0.781	0.784	0.756	0.986	0.905	0.020	N.A.	N.A.	N.A.	N.A.
	Tumor-only	Test set	0.865	0.791	0.791	0.800	0.825	0.806	0.892	0.015	N.A.	N.A.	N.A.	N.A.

ISSN: 1471-2105