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Classroom Contents
WGS Variant Calling - Variant Filtering and Annotation - Part 2 - Detailed NGS Analysis Workflow
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- 1 Intro
- 2 Overview of variant calling steps
- 3 Questions we may want to ask after calling variants
- 4 Variant data sources
- 5 Two approaches to filter variants
- 6 Hard filtering: Site-level filtering
- 7 Hard filtering: Sample-level filtering
- 8 Genotype Refinement
- 9 Data used for today’s demo
- 10 Pre-requisites
- 11 Filtering SNPs
- 12 Filtering INDELS
- 13 Understanding output after filtering FILTER column
- 14 Select variants that passed filters
- 15 Exclude variants that failed genotype filters
- 16 GATK Funcotator tool
- 17 Funcotator data sources
- 18 Annotate variants using Functotator
- 19 Understanding output after annotation Funcotator output
- 20 Getting annotations into a tabular format
