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Tutorial Details: 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.