Skip to main content

Table 4 Running times of the variant analysis workflow in different clouds

From: MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants

Exome (9.2 GB)
  Amazon Google Azure
Alignment (BWA) 0:12:20 0:18:40 00:26:00
IndelRealigner 0:14:39 0:20:10 00:28:00
MarkDuplicates 0:15:29 0:23:06 00:35:00
BQSR 0:28:06 0:34:15 00:55:00
HaplotypeCaller 1:08:46 0:58:40 01:28:00
GenotypeGVCFs 0:14:23 0:12:40 00:17:00
VQSR 0:10:07 0:10:14 00:12:00
Merge VCF 0:05:07 0:04:55 00:10:00
Convert VCF to Annovar 0:00:13 0:00:10 00:00:15
Annotate 0:05:16 0:05:36 00:09:00
Merge Annotation 0:03:06 0:04:01 00:06:00
Total 1:51:33 ($21.414) 2:06:28 ($13.94) 3:12:00 ($31.24)
Whole Genome (113 GB)
  Amazon Google Azure
Alignment (BWA) 8:03:53 8:10:13 11:18:20
IndelRealigner 3:04:03 3:09:34 04:15:58
MarkDuplicates 3:15:04 3:22:41 04:39:26
BQSR 4:11:14 4:17:23 06:35:44
HaplotypeCaller 9:05:43 9:15:49 14:29:22
GenotypeGVCFs 1:45:01 1:46:44 02:2:14
VQSR 1:33:29 1:33:36 02:05:13
Merge VCF 0:05:55 0:06:05 0:15:08
Convert VCF to Annovar 0:06:14 0:06:17 0:15:29
Annotate 0:15:01 0:15:21 0:24:39
Merge Annotation 0:10:06 0:11:01 0:23:07
Total 31:39:43 ($342.62) 32:13:06 ($208.07) 46:44:40 ($462)
  1. Running times (hours: minutes: seconds) of the variant analysis workflow in different clouds using a cluster of 4 nodes.  We give the time of different steps. The total time and cost (in USD) are in the rows titled “Total”. The best running times and options are underlined