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Tutorial Details: Galaxy DNA Variant Hands-on

Date: November 20, 01:00 PM - November 21, 04:00 PM,
Location: 575 Walter
Instructor(s): Dr. Joshua A Baller, , Dr. Innocent G Onsongo, MSI

This two day tutorial (held from 1:00pm to 4:00pm on both days, Nov 20 & 21) covers topics typical of sequencing experiments in eukaryotic species with high-quality genomes and genome annotation available. Participants are expected to be familiar with next-generation sequence data and basic theory of variant detection. Participants will perform analyses from start to finish with the goal of identifying SNP variants using data from a de-identified human DNA sample. This will include (1) sample QA/QC, (2) mapping via BWA, (3) post-processing of alignment files to remove PCR duplicates, re-calibrate basecalls and cleanup regions near indels, (4) genotype calling, (5) SNP annotation, and (6) SNP filtering and quality re-calibration.

Prerequisites: GALAXY 101 or experience with GALAXY, and the Galaxy DNA Variant