Table 2 Run time of the variant calling process for the eight variant calling tools investigated regarding the first and second dataset.
From: Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data
Variant caller | Preprocessing | CPU time (first dataset) | CPU time (second dataset) | Option for multithreading |
|---|---|---|---|---|
GATK | yes | 1,021 min | 4,876 min | yes |
Platypus | no | 59 min | 9,952 min | yes |
VarScan | yes | 649 min | 2,906 min | no |
LoFreq | yes | 945 min | 11,991 min | yes |
FreeBayes | no | 732 min | 6,652 min | no |
SNVer | no | 492 min | 14,431 min | no |
SAMtools | yes | 305 min | 1,859 min | no |
VarDict | no | 281 min | 3,513 min | no |
