Table 3 Descriptive statistics of GATK filters in the LC dataset, stratifying calls by type (SNV/Indels). Data are displayed as mean ± sd
SNVs | Indels | |||||
|---|---|---|---|---|---|---|
TV mean ± sd | FV mean ± sd | p-value | TV mean ± sd | FV mean ± sd | p-value | |
BQRS | 0.02 ± 0.02 | -0.27 ± 0.12 | <0.0001 | 0.16 ± 0.16 | 0.01 ± 0.03 | <0.0001 |
RPRS | -0.19 ± 0.03 | -0.31 ± 1.1 | <0.0001 | -1.29 ± 0.3 | 0.04 ± 0.04 | <0.0001 |
CRS | -0.02 ± 0.02 | -0.05 ± 0.07 | <0.0001 | -0.004 ± 0.12 | -0.04 ± 0.01 | 0.001 |
DP | 19.97 ± 0.17 | 22.72 ± 1.3 | <0.0001 | 21.83 ± 1.97 | 20.24 ± 0.42 | <0.0001 |
MQ | 60 ± 0 | 60 ± 0 | - | 60 ± 0 | 60 ± 0 | - |
MQRS | -0.06 ± 0.01 | -0.1 ± 0.08 | <0.0001 | -0.15 ± 0.15 | -0.1 ± 0.04 | 0.03 |
GQ | 99 ± 0 | 20.04 ± 2.9 | - | 99 ± 0 | 17.94 ± 0.92 | - |