scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing

Table 1 Accuracy metric summaries for alignment and SNV calling algorithms

SNV caller	Metric	scSNV Collapsed	scSNV Tags	Cell Ranger	STARsolo
scSNV Pileup	TPR	0.954 ± 0.005	0.953 ± 0.005	0.94 ± 0.011	0.955 ± 0.005
scSNV Pileup + AF cutoff	TPR	0.934 ± 0.009	0.918 ± 0.016	0.899 ± 0.012	0.912 ± 0.013
samtools/bcftools	TPR	0.819 ± 0.031	0.819 ± 0.03	0.81 ± 0.023	0.821 ± 0.028
Strelka2	TPR	0.037 ± 0.014	0.115 ± 0.025	0.11 ± 0.019	0.110 ± 0.02
scSNV Pileup	FDR	0.430 ± 0.052	0.547 ± 0.041	0.734 ± 0.055	0.729 ± 0.057
scSNV Pileup + AF cutoff	FDR	0.108 ± 0.029	0.109 ± 0.031	0.331 ± 0.038	0.322 ± 0.044
samtools/bcftools	FDR	0.049 ± 0.015	0.048 ± 0.014	0.178 ± 0.035	0.152 ± 0.027
Strelka2	FDR	0.039 ± 0.019	0.032 ± 0.015	0.052 ± 0.02	0.053 ± 0.018
scSNV Pileup	F1	0.713 ± 0.04	0.613 ± 0.038	0.412 ± 0.067	0.419 ± 0.07
scSNV Pileup + AF cutoff	F1	0.912 ± 0.017	0.904 ± 0.021	0.767 ± 0.028	0.777 ± 0.03
samtools/bcftools	F1	0.880 ± 0.021	0.880 ± 0.020	0.816 ± 0.025	0.834 ± 0.021
Strelka2	F1	0.071 ± 0.026	0.204 ± 0.041	0.197 ± 0.031	0.196 ± 0.032

ISSN: 1474-760X