Welcome to the Variant Data Import and Analysis Tutorial

Updated: February 7th, 2012

Level: Advanced

Packages: DNA-Seq, Power Seat

Contents: Jump to Table of Contents

This tutorial covers a comprehensive sequencing analysis workflow for importing VCF files, performing quality assurance, and running association tests on sequence data and a simulated phenotype.

Requirements

To complete this tutorial you will need to download and unzip the following file, which includes several datasets.

Download

1kGenomes_Data_Phenotype.zip

Files included in the above ZIP file:

• VCF Files - Partial exon sequence data for 697 subjects from the 1000 Genomes Pilot3 project (March 2010 data release)
• Phenotype - Simulated phenotype data in .csv format

Download

Download entire tutorial in PDF format

Table of Contents:

• 1. Overview
• 2. Import VCF and Phenotype Files
  • A. Import Phenotype CSV
  • B. Import VCFs from one or more files script
  • C. Download Annotation Tracks to Local Machine
• 3. Filtering and Collapsing Rare Variants
  • A. Filtering on Total Per Genotype Read Depth
  • B. Filtering on SIFT Score
  • C. Detect the Presence of a Variant in a Gene
  • D. Count Number of Variants (Per Gene)
• 4. Variant Frequency Binning and CMC Method
  • A. Create Frequency Bins
  • B. CMC Method
  • C. CMC Method with Regression
  • D. CMC Method with Regression Using Transcripts
• 5. KBAC Method
  • A. KBAC with Permutation Testing
  • B. KBAC with Regression
  • C. KBAC for Lower Sample Risk
• 6. Compare Results with GWAS Approach
  • A. Perform a Genotype Association Test
  • Conclusion
  • References