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Tutorial Registration: Two-day Workshop - SNP Variant Detection Applied Tutorial - Using the Genome Analysis Tool Kit (GATK) Best-practices Pipeline

Date: Tuesday, February 12, 2013, 01:00 pm - 04:00 pm
Location: 575 Walter
Instructor(s): Kevin A. T. Silverstein, MSI, Ying Zhang, MSI, Dr. Getiria Onsongo, MSI

This is a two-day workshop. Attendance is required on both February 12 and 13 (1:00 to 4:00 both days).

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).

In this hands-on tutorial, participants will perform analyses from start to finish with the goal of identifying SNP variants using data from de-identified human DNA samples. This will include (1) sample QA/QC, (2) mapping via BWA, post-processing of alignment files to remove PCR duplicates, re-calibrate basecalls and cleanup regions near indels, (3) genotype calling, (4) SNP annotation, and (5) SNP filtering and quality re-calibration.

The first half hour of the first session will cover the basics of the Galaxy interface, so those already familiar with Galaxy can safely arrive one half-hour late for the first session.

Level: Intermediate
Prerequisites: See note on Galaxy in last paragraph of description.
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This event is currently full. You may register and be added to the list. If a place becomes available IT WILL BE RESERVED FOR YOU and you will be notified.

If you will not be able to attend, please cancel your reservation to make room for others. Your confirmation email will include a cancellation link.