Table 1 Timing results for stages in the clair3-npore-hap pipeline (Table 3)
From: nPoRe: n-polymer realigner for improved pileup-based variant calling
Step | Real time | CPU time |
|---|---|---|
*Align reads | 1218:01 | 7808:24 |
Generate tensors | 44:29 | 301:53 |
Train clair3 | 38:18 | 54:22 |
Call variants | 86:26 | 2392:17 |
Phase variants | 347:58 | 344:05 |
*Phase reads | 240:32 | 228:03 |
*Index BAM | 1138:09 | 1750:13 |
Phase truth VCF | 364:23 | 360:03 |
Standardize truth VCF | 546:31 | 3756:46 |
*Realign reads | 2168:15 | 111,792:55 |
*Generate haplotype tensors | 1363:23 | 3162:48 |
Train model | 41:40 | 66:29 |
Call variants | 200:08 | 8343:01 |