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Tutorial Registration: Intro to Variant Detection with the Genome Analysis ToolKit (GATK)

Date: Wednesday, November 6, 2013, 09:00 am - 11:00 am
Location: 402 Walter
Instructor(s): Kevin A. T. Silverstein, MSI

DNA resequencing with the intent to identify single nucleotide polymorphisms in individual samples is emerging as a frequent core task to identify genotypic differences in a population that may contribute to important phenotypic effects. The computational field has converged on a standardized best practices suite of tools for analyzing this type of data centered around the Genome Analysis Toolkit (GATK). This lecture-style tutorial will cover the background material necessary for investigators who are just entering the field, and will serve as a good introduction to the more in-depth hands-on tutorial that follows.

General topics covered will include: Basic background on Next-Generation Sequencing (NGS) DNA-Seq experimental protocols and data formats (e.g., fastq, SAM, BAM, VCF), overview of high-level project strategies (e.g., whole genome resequencing, hybridization capture, amplicon sequencing approaches, and pooling strategies), fundamental steps in analysis, design concerns and recommendations for different organism characteristics (e.g., diploid bi-allelic, polyploid, aneuploid, multi-allelic) and internal and external resources for subsequent consultation.

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Prerequisites:
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