GASystemChannel
－GA04 GATK-序列比對 (coming soon)
Environment requirement
- Hardware : CPU : 10 cores
- RAM : 45 Gb
- Software :The pipeline is developed based on GA System. All software used in the pipeline are included in pre-defined software environments (GA application collection ). Please install suitable environment before start the pipeline(How to do it!) .
The diagram of workflow
Reference
For GATK
| Homo_sapiens | Path | Source |
| GATK_b37 | /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/b37 | GATK_Resource_bundle |
| GATK_hg19 | /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/hg19 | GATK_Resource_bundle |
| GATK_hg38 | /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/hg38 | GATK_Resource_bundle |
| GATK_Mutect2 | /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/Mutect2 | GATK_Mutect2 |
For annovar
| Homo_sapiens | Path | Source |
| ANNOVAR_hg19 | /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg19 | Annovar |
| ANNOVAR_hg38 | /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg38 | Annovar |
For SnpEff
| SnpEff_GRCh37.87 | /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCh37.87 | SnpEff |
| SnpEff_GRCh38.99 | /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCh38.99 | SnpEff |
| SnpEff_GRCm38.99 | /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCm38.99 | SnpEff |
For SnpSift
| dbNSFP4.1a | /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/ | SnpSift |