Table 3 Number of false-negatives when different steps in the pipeline omitted
From: Edge effects in calling variants from targeted amplicon sequencing
u(minimum distance of the Uracil base from 3’ end of primer) | No. of simulated variants | False-negatives | |||
|---|---|---|---|---|---|
| Â | Â | Without BAQ and BQSR | With BQSR and without BAQ | With BAQ and without BQSR | Default pipeline (with both BAQ and BQSR) |
1 | 15,871 | 8 | 669 | 3,725 | 2,830 |
2 | 15,871 | 9 | 23 | 775 | 397 |
3 | 15,871 | 3 | 3 | 136 | 37 |
4 | 15,871 | 1 | 1 | 59 | 13 |
5 | 15,871 | 0 | 0 | 35 | 5 |
6 | 15,871 | 0 | 0 | 20 | 2 |
7 | 15,871 | 0 | 0 | 23 | 1 |
8 | 15,871 | 0 | 0 | 28 | 0 |