Table 2 Effect of BQSR in SNP and INDEL calling
From: Impact of post-alignment processing in variant discovery from whole exome data
Type | Metric | Div | 5x coverage | 40x coverage | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
(%) | Case | Min | Max | Mdn | Case | Min | Max | Mdn | ||
SNP | Sensitivity | 0.05–0.1 | 50 | −0.1 | 1.6 | 0.6 | 50 | 0 | 0.2 | 0 |
SNP | Sensitivity | 0.5–1 | 50 | −4.5 | 0.9 | −0.6 | 50 | −0.5 | 0.1 | −0.1 |
SNP | Sensitivity | 5 | 20 | −11.4 | −2.6 | −9.8 | 20 | −1.8 | 0.2 | −0.5 |
SNP | Sensitivity | 10 | 20 | −57.8 | −19.5 | −32.3 | 20 | −89.4 | 3 | −7.1 |
SNP | Precision rate | 0.05–1 | 100 | −0.1 | 0.3 | 0 | 100 | −0.2 | 0.1 | 0 |
SNP | Precision rate | 5 | 20 | 0 | 0.3 | 0.1 | 20 | 0 | 0.2 | 0 |
SNP | Precision rate | 10 | 0 | - | - | - | 18 | −0.3 | 1.5 | 0.2 |
INDEL | Sensitivity | 0.05–0.1 | 40 | −1.5 | 1.8 | 0.4 | 50 | −0.2 | 0 | 0 |
INDEL | Sensitivity | 0.5–1 | 40 | −0.3 | 1 | 0.1 | 50 | −0.1 | 0.1 | 0 |
INDEL | Sensitivity | 5 | 12 | −6.4 | −0.1 | −1.4 | 20 | −0.9 | 2.8 | 0 |
INDEL | Sensitivity | 10 | 12 | −51.9 | −2.4 | −34.6 | 16 | −75.3 | 0.1 | −9.7 |
INDEL | Precision rate | 0.05–1 | 80 | −0.1 | 0 | 0 | 100 | −0.1 | 0.2 | 0 |
INDEL | Precision rate | 5 | 12 | 0 | 0.3 | 0 | 20 | 0 | 0.8 | 0 |
INDEL | Precision rate | 10 | 0 | - | - | - | 13 | −0.2 | 3.2 | 0 |