BroadE Workshop 2013 Oct 21-22: GATK Best Practices & Queue
GATK Best Practices & Queue


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Summary


This workshop included two modules:

  • Best Practices for Variant Calling with the GATK

    The core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. View the workshop materials to learn why each step is essential to the calling process, what are the key operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.

  • Building Analysis Pipelines with Queue

    An introduction to the Queue pipelining system. View the workshop materials to learn about how to use Queue to create analysis pipelines, scatter-gather them and run them locally or in parallel on a computing farm.


= presentation slides | = video recording


Workshop materials


Best Practices for Variant Calling with the GATK

Day 1 - Opening remarks
Introduction to Next Generation Sequence Analysis
Introduction to the GATK
Mapping and duplicate marking (data pre-processing)
Local realignment around indels RTC IR
Base quality score recalibration (BQSR) BR PR
Compression with ReduceReads RR
Variant calling UG HC
Variant quality score recalibration (VQSR) VR AR
Genotype phasing and refinement PBT RBP
Functional annotation VA
Analyzing variant calls SV CV VE
Introduction to Parallelism NT NCT Q

Building Analysis Pipelines with Queue

Day 2 - Opening remarks
Introduction to Queue Q
Queue 101: the basics Q
Parallelism with Queue Q
Advanced Queue capabilities Q

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