Table 1.
Examples of processing of 31-GB BAM and matching 11-GB CRAM of HG00110 with sambamba and samtools. Wall-clock time (t in seconds) reflects improved analysis time. CPU (×100%) reflects effective multi-core utilisation. See Figure 1 caption for description of hardware, software and measurements
| samtools t(s) CPU% | Sambamba t(s) CPU% | Speedup | |||
|---|---|---|---|---|---|
| BAM view | 1506 | 429 | 785 | 3.5× | |
| Filtera | 195 | 35 | 471 | 3.5× | |
| Sort | 12 288 | 396% | 1265 | 945 | 10× |
| Index | 577 | 137 | 562 | 4× | |
| Markdupb | 5220 | 2296 | 278 | 2× | |
| Merge | 3090 | 571% | 2247 | 1015 | 1.5× |
| mpileupc | 7750 | 584 | 4409 | 13× | |
| BAM to CRAM | 4354 | 640 | 796 | 7× | |
| CRAM to SAM | 1850 | 729 | 347 | 2.5× | |
| CRAM index | 9 | 9 | = | ||
aFilter on q > 30 and Chr1.
bFor markdup samtools v0.19 was used.
cmpileup to VCF on 2GB BAM of Chr1 only.