Table 3.
Effects of duplicate marking, realignment & recalibration on SNP calling accuracy
| Call set | Site discovery | |||||
|---|---|---|---|---|---|---|
| No. SNPs | Ti/Tv ratio | |||||
| All | Known | Novel | dbSNP% | Known | Novel | |
| Deep coverage with QUAL > 50 | ||||||
| initial | 96472 | 71534 | 24938 | 74.15% | 2.50 | 1.73 |
| realignment | 94595 | 71374 | 23221 | 75.45% | 2.50 | 1.84 |
| recalibration | 96316 | 71518 | 24798 | 74.25% | 2.50 | 1.75 |
| mark duplicate | 96303 | 71502 | 24801 | 74.24% | 2.50 | 1.73 |
| Shallow coverage with QUAL > 20 | ||||||
| initial | 780490 | 607178 | 173312 | 77.79% | 2.13 | 1.39 |
| realignment | 776560 | 606806 | 169754 | 78.14% | 2.13 | 1.41 |
| recalibration | 783387 | 609601 | 173786 | 77.81% | 2.13 | 1.40 |
| mark duplicate | 738198 | 583829 | 154369 | 79.09% | 2.13 | 1.53 |
SNPs were called for 5 samples together by GATK using bases with base quality≥20 and reads with mapping quality ≥20. Only sites with QUAL > 50 for deep-coverage or QUAL > 20 for shallow coverage were considered as potentially variable sites.