Topic: Variant Analysis

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Session Description
QIAGEN’s CLC Genomics Workbench enables researchers to analyze NGS data without the use of command line and is a powerful tool for determining differential expression and for variant calling. In this workshop students will explore the usage of CLC Genomics Workbench for taking raw NGS data and performing QC, processing, statistical analyses, and visualizations. The first part of the training will focus on the identifying differentially expressed genes from RNA-seq and how those results can be passed to Ingenuity Pathway Analysis (IPA) for biological interpretation. The second half of the training will provide insight into analysis of DNA-seq data for variant detection and will introduce how Ingenuity Variant Analysis (IVA) can be used to prioritize those variant findings.

Meeting Link: https://btep.ccr.cancer.gov/classes/variant-2/

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Presenter: Justin Lack (NIAID CBR)

1.Experimental Design Considerations in Variant Analysis

i. Germline vs Somatic

ii. WGS vs WES

iii. Sample sizes and statistical power

2. WGS/WES Pipelines at NIH

i. Pipeline Performance

ii. Using Pipeliner for internal and external data

3. Variant QC, Annotation and Downstream Analysis

i. Variant QC and data correction

ii. Variant annotation and analysis tools

4.  Structural variation and multi-omic integration