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Table 1 Accuracy metric summaries for alignment and SNV calling algorithms

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

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