Table 2.
Quality control (QC) steps for variants and samples. The workflow resulted in 16,934 high-quality variants for 255 high-quality samples.
| Type | QC Step | Passed n (%) | Excluded n (%) |
|---|---|---|---|
| Variant QC | 2,309,151 | ||
| 1. Hard filters | 2,028,582 (87.8%) | 280,569 (12.2%) | |
| 2. Missingness | 124,078 (7%) | 1,904,504 (93%) | |
| 3. Genotype quality (GQ) filter | 89,614 (72.3%) | 34,464 (27.7%) | |
| 4. Minor allele frequency (MAF) | 17,961 (20%) | 71,923 (80%) | |
| 5. Hardy Weinberg Equilibrium | 16,934 (95.7%) | 757 (4.3%) | |
| 16,934 | |||
| Samples QC | 268 | ||
| 6. Missingness | 268 (>99%) | 1 (<1%) {1 nrPC} | |
| 7. Heterozygosity | 265 (99%) | 3 (1%) {1 nrPC, 1 rPDAC and 1 CP} | |
| 8. Relatedness | 260 (98%) | 5 (2%) {3 nrPC, and 2 CP} | |
| 9. Stratification | 255 (98%) | 5 (2%) {2 nrPC, 1 rPDAC and 2 CP} | |
| 255 |