From: Reducing INDEL calling errors in whole genome and exome sequencing data
Concordance rate | Without filtering | ≥1 read | ≥20 reads | ≥40 reads | ≥60 reads | ≥80 reads |
---|---|---|---|---|---|---|
Exact-match | 53% (0.8%) | 62% (1.1%) | 69% (1.5%) | 73% (2.3%) | 76% (1.6%) | 74% (1.3%) |
Position-match | 55% (0.8%) | 66% (1.0%) | 73% (1.1%) | 77% (1.8%) | 79% (1.1%) | 76% (1.3%) |
Discordance rate | Without filtering | ≥1 read | ≥20 reads | ≥40 reads | ≥60 reads | ≥80 reads |
WGS-specific | 34% (1.4%) | 20% (1.5%) | 14% (1.6%) | 14% (2.2%) | 15% (2.5%) | 20% (3.2%) |
WES-specific | 11% (1.2%) | 14% (1.4%) | 13% (1.3%) | 9% (2.6%) | 6% (2.2%) | 4% (1.5%) |