2013年9月14日星期六

BroadE Workshop 2013 July 9-10

http://www.broadinstitute.org/gatk/guide/events?id=3093#materials

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.

Workshop materials


 - 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 (video not available yet)
NT NCT Q



Supplemental materials


 -  - 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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