Bamtocov
Andrea Telatin edited this page Oct 29, 2021
·
3 revisions
covtobed algorithm is being ported to Nim
Human targeted sequencing of 16 genes (panel)
| Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
|---|---|---|---|---|
bamtocov-2.0.2 "panel_01.bam" |
505.8 ± 6.8 | 500.1 | 515.9 | 1.41 ± 0.07 |
bamtocov-2.0.4 "panel_01.bam" |
409.6 ± 13.7 | 394.8 | 430.4 | 1.14 ± 0.07 |
bamtocov-2.1.0 "panel_01.bam" |
390.1 ± 9.7 | 375.5 | 400.1 | 1.09 ± 0.06 |
bamtocov-2.1.0-nimble "panel_01.bam" |
358.9 ± 18.3 | 341.6 | 387.9 | 1.00 |
bamtocov-2.1.0-nim "panel_01.bam" |
436.0 ± 12.8 | 411.7 | 445.9 | 1.21 ± 0.07 |
covtobed-1.2 "panel_01.bam" |
533.2 ± 8.8 | 527.1 | 548.4 | 1.49 ± 0.08 |
megadepth-1.1.2 --coverage "panel_01.bam" |
9246.8 ± 1509.7 | 8026.7 | 11072.8 | 25.77 ± 4.41 |
mosdepth-0.3.1 /tmp/prefix "panel_01.bam" |
53499.6 ± 875.1 | 52284.1 | 54548.5 | 149.08 ± 7.97 |
Human exome, subsampled, only Chromosome 2
| Command | Mean [s] | Min [s] | Max [s] | Relative |
|---|---|---|---|---|
bamtocov-2.0.2 "HG00258.04-chr2.bam" |
36.281 ± 0.537 | 35.707 | 36.771 | 4.17 ± 0.06 |
bamtocov-2.0.4 "HG00258.04-chr2.bam" |
43.611 ± 1.167 | 42.297 | 44.529 | 5.01 ± 0.14 |
bamtocov-2.1.0 "HG00258.04-chr2.bam" |
43.888 ± 0.797 | 43.371 | 44.805 | 5.04 ± 0.09 |
bamtocov-2.1.0-nimble "HG00258.04-chr2.bam" |
18.416 ± 0.863 | 17.465 | 19.149 | 2.12 ± 0.10 |
2.1.0-nimc "HG00258.04-chr2.bam" |
43.696 ± 0.269 | 43.409 | 43.942 | 5.02 ± 0.03 |
covtobed-1.2 "HG00258.04-chr2.bam" |
24.794 ± 0.469 | 24.340 | 25.278 | 2.85 ± 0.05 |
megadepth-1.1.2 --coverage "HG00258.04-chr2.bam" |
8.706 ± 0.028 | 8.687 | 8.738 | 1.00 |
mosdepth-0.3.1 /tmp/prefix "HG00258.04-chr2.bam" |
19.134 ± 1.330 | 17.609 | 20.056 | 2.20 ± 0.15 |
Covtobed - Wiki - a simple tool to extract BED coverage tracks from BAM files