| Â | SAMtools | GATK | ANGSD | GATK (2cores) | ANGSD (2cores) | GATK (4cores) | ANGSD (4cores) |
|---|
50 Samples | 2722 | 1706 | 602 | 1744 | 1171 | 1765 | 1646 |
100 Samples | 5097 | 4049 | 1270 | 4143 | 2457 | 4373 | 4013 |
200 Samples | 10615 | 9672 | 2704 | 9951 | 5032 | 10330 | 7352 |
- Wallclock time (not CPU) measured in seconds for different samples sizes and different number of allocated cores. Commands used are found in Additional file 7. We did the analysis twice (in different order) and picked the lowest value. Notice that the runtime for GATK and ANGSD does not decrease with 2 and 4 threads. This could be an indication that the file reading is the bottleneck.
