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H3ABioNet SOPs
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Organization
Genomic Analyses
Human variant calling
Genome Wide Association Studies
RNA Sequencing data analysis
16S Diversity analysis
Contributing
Technical Guide
Language & Style
Feedback
Variant-Calling SOP 7.0
Introduction
Introduction
Glossary of associated terms and jargon
Overall procedure
Important note
Phase I. Preprocessing raw reads
Adaptor trimming
Quality trimming
Removal of very short reads
Phase II. Initial variant discovery
Alignment and Deduplication
Local realignment around indels
Base quality score recalibration
Calling the variants
Statistical Filtering
Phase III. Variant annotation and prioritization
Annotation and prioritization
H3ABioNet Accreditation exercise
Training dataset
Accreditation Questions
Appendices
Useful Resources
List of tools
Variant calling in human whole genome/exome sequencing data
Edit me
Appendices
Bibliography
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