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MorrellLAB / sequence_handling Public

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Recommended_Workflow

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Paul Hoffman edited this page Aug 5, 2015 · 15 revisions

Recommended Worklfow

Workflow

Next: `sample_list_generator.sh`

Toggle table of contents Pages 23

Home
Adapter_Trimming
Configuration
Coverage_Mapping
Create_HC_Subset
Dependencies
FAQ
Genomics_DB_Import
Genotype_GVCFs
Haplotype_Caller
Indel_Realigner
Pre_Variant_Filtering
Quality_Assessment
Quality_Trimming
Read_Mapping
Realigner_Target_Creator
Recommended_Workflow
SAM_Processing
sample_list_generator.sh
Slurm specific options
Variant_Analysis
Variant_Filtering
Variant_Recalibrator

Main Information

Getting Started
Recommended Workflow
Configuration
Dependencies
sample_list_generator.sh
Slurm specific options
Common Problems and Errors

Recommended Workflow Handlers

1. Quality Assessment
2. Adapter Trimming
3. Read Mapping
4. SAM Processing
5. Coverage Mapping
6. Haplotype Caller
7. GenomicsDBImport
8. Genotype GVCFs
9. Create HC Subset
10. Variant Recalibrator
11. Pre-Variant Filtering
12. Variant Filtering
13. Variant Analysis

Other Handlers

Quality Trimming
Realigner_Target_Creator
Indel_Realigner

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