This is the github repository for the Eichler lab Amazon Web Services (AWS) pipelines
| Pipeline | Analysis type | Instance type | Instance cost per hour ($) | Volume size | Volume cost per hour ($) | Number of cores on instance | Memory (GB) on instance | Number of samples run in test | Actual hours to run | cpu hours by analysis type | cpu hours by sample | cost per sample ($) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| FreeBayes | Family | m4.10xlarge | 2.394 | 1 x 1000 GB | 0.13 | 40 | 160 | 4 | 8 | 320 | 80 | 5.05 |
| GATK | Family | m4.10xlarge | 2.394 | 1 x 1000 GB | 0.13 | 40 | 160 | 4 | 20 | 800 | 200 | 12.62 |
| mrssnake mapping | Sample | m4.10xlarge | 2.394 | 1 x 1000 GB | 0.13 | 40 | 160 | 1 | 13 | 680 | 680 | 32.81 |
| Lumpy | Family | m4.xlarge | 0.239 | 1 x 1000 GB | 0.13 | 4 | 16 | 4 | 8 | 24 | 8 | 0.74 |
| QC | Sample | m4.2xlarge | 0.479 | 1 x 1000 GB | 0.13 | 8 | 32 | 4 | 7 | 56 | 14 | 1.07 |
| VariationHunter | Family | m4.2xlarge | 0.479 | 1 x 1000 GB | 0.13 | 8 | 32 | 4 | 8 | 64 | 16 | 1.22 |
| Wham | Family | m4.2xlarge | 0.479 | 1 x 1000 GB | 0.13 | 8 | 32 | 4 | 6 | 48 | 12 | 0.91 |
| Whamg | Family | m4.2xlarge | 0.479 | 1 x 1000 GB | 0.13 | 8 | 32 | 4 | 4 | 32 | 8 | 0.61 |
| SVTyper | Family | m4.xlarge | 0.239 | 1 x 1000 GB | 0.13 | 4 | 16 | 4 | 19 | 76 | 19 | 1.75 |
- Note: QC includes Picard Hybridization Metrics, Picard WGS Metrics, Flagstat, Wham to calculate insert size median and standard deviation, Samtools to extract mitochondria. For mrssnake pipeline please see https://github.com/bnelsj/mrssnake.git