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Tutorial Details: SNP Variant Detection Analysis Background and Theory

Date: Tuesday, January 29, 2013, 01:15 pm - 02:45 pm
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.

Tutorial slides are largely based on The Broad’s BroadE Workshop 2012 Dec 4-5 posted at http://www.broadinstitute.org/gatk/guide/events?id=2038#materials.

Level: Introductory
Prerequisites: Basic knowledge of molecular biology and genetics