Table 1 Percent of SNP and INDEL calling sensitivity in simulated data
From: An analytical workflow for accurate variant discovery in highly divergent regions
Type | Div | Cov | Caller | ||||
|---|---|---|---|---|---|---|---|
(%) | GATK UG | Platypus | SAMtools | GATK HC | FreeBayes | ||
SNP | 0.05–1.00 | 10 | 87.3–89.8 (A) | 77.6–83.0 (C) | 85.9–88.4 (B) | 85.4–87.3 (B) | 84.1–88.1 (B) |
SNP | 0.05–1.00 | 40–100 | 96.0–98.5 (A) | 87.6–96.0 (D) | 95.3–98.2 (B) | 95.3–97.4 (C) | 93.3–98.6 (C) |
SNP | 5.00–10.00 | 10 | 82.2–88.0 (A) | 43.7–59.4 (E) | 80.7–85.5 (B) | 73.6–84.0 (C) | 61.3–74.3 (D) |
SNP | 5.00–10.00 | 40–100 | 91.3–97.4 (A) | 42.0–64.1 (E) | 90.8–95.1 (B) | 85.7–95.3 (C) | 65.6–81.6 (D) |
INDEL | 0.05–1.00 | 10 | 42.0–53.5 (D) | 69.1–74.9 (A) | 63.2–73.1 (C) | 69.7–74.5 (A) | 67.5–75.3 (B) |
INDEL | 0.05–1.00 | 40–100 | 74.2–82.9 (C) | 77.8–85.5 (A) | 72.6–82.9 (C) | 77.9–83.3 (B) | 76.0–84.0 (B) |
INDEL | 5.00–10.00 | 10 | 37.4–47.4 (D) | 64.1–70.9 (A) | 13.3–47.7 (E) | 58.4–69.0 (B) | 55.5–65.5 (C) |
INDEL | 5.00–10.00 | 40–100 | 70.5–79.7 (B) | 72.8–81.7 (A) | 23.6–64.1 (D) | 70.8–78.6 (B) | 62.4–73.7 (C) |