BroadE Workshop 2013 July 9-10: Best Practices for Variant Calling with the GATK
Best Practices for Variant Calling with the GATK


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Summary


This workshop covered 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.


= 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
Day 2 - Opening remarks
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

Third-Party Tools: GenomeSTRiP and XHMM

GenomeSTRiP: Discovery and genotyping of deletions
XHMM: Discovery and genotyping of copy number variation from exome read depth (PDF not available for download yet)

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