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 | 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 | 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) |