Table 4.

Computational speed of GATK,SAMtools and ANGSD

	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.