MPG Next-Generation DNA sequencing tutorials

GSA next-generation sequencing tutorials

• File:Ngs tutorial depristo 1210.pdf: Data processing and analysis of genetic variation using next-generation sequencing -- Mark DePristo

Video of the talk can be found as part of the MPG Primer series

GSA Feb. 17th 2011 next-generation sequencing workshop

On Feb. 11th, 2011 GSA organized a next-generation sequencing workshop at the Broad institute. The topcs and speakers were:

• Overview -- Mark DePristo
• Mapping, Alignment, SNP calling -- Heng Li
• SNP calling and error modeling - Ryan Poplin
• Indel Calling Pipeline in the GATK - Guillermo del Angel
• Read-backed haplotype phasing - Menachem Fromer
• Discovering and genotyping deletions using GenomeSTRiP - Bob Handsaker
• The Picard Pipelines -- Tim Fennell
• QPipeline: variant calling pipeline for custom-target, exome, and deep whole-genomes - Kiran Garimella
• GATK-Queue: Command-line job manager and scripting framework for multi-stage genomic analysis - Khalid Shakir
• Analysis of genetic variation data from large-scale, population-based medical sequencing studies - Shaun Purcell

All of the talks can be obtained from the GSA Public Drop Box

GSA Feb. 4th 2010 next-generation sequencing workshop

On Feb. 4th, 2010 GSA organized a next-generation sequencing workshop at the Broad institute. The topcs and speakers were:

• NGS Project Management -- Carrie Sougnez
• MAQ/BWA -- Heng Li
• The Picard Pipeline -- Tim Fennell
• Base Quality Score Recalibration - Ryan Poplin
• Quality Assessment of Hybrid Selection Experiments - Kristian Cibulskis and Andrew Kernytsky
• Indel Cleaning and Calling - Andrey Sivachenko and Eric Banks
• SNP Calling - Mark DePristo
• Quality Assessment of SNP Calls - Kiran Garimella
• Pooled SNP Calling - Jason Flannick
• Visualizing NGS with IGV - Jim Robinson