Module-01-Setup

• Intro to Precision Medicine

• AWS Intro

• AWS Instance Setup

• UNIX Primer

• Installation

• Environment

• Directory Setup

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Module-02-Inputs

• Intro to References, Annotations, and Raw Data

• Reference Genome

• Annotation

• Indexing

• Data

• PreAlignment QC

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Module-03-Align

• Intro to Alignment Algorithms, Visualization, and QC

• Alignment

• Intro to IGV

• Post Alignment Visualization

• Post-Alignment QC

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Module-04-Germline

• Intro to Germline WGS and Exome Variant Analysis

• Germline SNV and Indel Calling

• Germline SNV/Indel Filtering/Annotation/Review

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Module-05-Somatic

• Intro to Somatic WGS and Exome Variant Analysis

• Somatic SNV/InDel Calling

• Somatic SNV and Indel Filtering and Annotation

• Somatic SNV and Indel Manual Review

• Somatic SV Calling

• Somatic SV Filtering/Annotation/Review

• Somatic CNV Calling

• Somatic CNV Filtering/Annotation/Review

• Somatic LOH Calling

• Somatic LOH Filtering/Annotation/Review

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Module-06-RNAseq

• Intro to RNAseq Analysis

• RNAseq Expression Estimation

• RNAseq Differential Expression

• RNAseq Differential Expression Visualization

• Reference Free Expression Analysis with Kallisto

• RNAseq Fusion Calling

• RNAseq Fusion Filtering/Annotation/Review

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Module-07-Clinical

• Intro to Clinical Applications

• Germline Variant Interpretation

• Somatic Variant Interpretation

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Module-08-Immune

• Intro to Immunogenomic Analysis

• Personalized Cancer Vaccine Design

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Module-09-CWL

• Intro to the Common Workflow Language

• Installing the Common Workflow Language

• The Workflow File

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Module-10-Appendix

• Intro to Appendix and Additional Resources

• Developer Notes

• AWS AMI Setup

• DNA alignment lab

• Team Exercise DNA alignment

• ChIP-seq analysis

• R visualization - ggplot2

• Data munging / cleaning