Table 1 Average running time spent in calling indels for samples with low/high coverage
From: Performance evaluation of indel calling tools using real short-read data
Tool | Time | |
|---|---|---|
Low Coverage (~6X) | High Coverage (~64X) | |
GATK_UG | 16 minutes 43 seconds | 24 minutes 19 seconds |
VarScan | 16 minutes 1 second | 84 minutes 02 seconds |
Pindel | 25 minutes 36 seconds | 139 minutes 09 seconds |
SAMtools | 11 minutes 26 seconds | 64 minutes 14 seconds |
Dindel | 165 minutes 22 seconds | 1549 minutes 18 seconds |
GATK_HC | 58 minutes 27 seconds | 91 minutes 13 seconds |
Platypus | 3 minutes 36 seconds | 5 minutes 59 seconds |