Tutorial Details: Two-day Workshop - SNP Variant Detection Applied Tutorial - Using the Genome Analysis Tool Kit (GATK) Best-practices Pipeline
|Date:||Wednesday, November 28, 2012, 01:00 pm - 04:00 pm|
|Instructor(s):||Kevin A Silverstein PhD, MSI, John R Garbe, MSI, Dr. Getiria Onsongo, MSI|
**This is a two-day workshop. Attendance is required on both November 28 and 29 (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.
|Prerequisites:||See note on Galaxy in last paragraph of description.|