[BBC] Workshop GATK Best Practices for Variant Discovery, 17-19 July 2017 - Registration open (second announcement)

[Bert Overduin]

Dear all,

I am happy to announce that for the third year in a row we have been able
to get three members of the GATK team of the Broad Institute (
https://software.broadinstitute.org/gatk/) over to Edinburgh for a few days
to teach a workshop on GATK Best Practices for Variant Discovery.

Details of the workshop can be found below.

With kind regards,
Bert

**********

GATK BEST PRACTICES FOR VARIANT DISCOVERY

DATE: Monday 17 - Wednesday 19 July 2017
VENUE: The King's Buildings,The University of Edinburgh, Edinburgh,
Scotland, UK
REGISTRATION DEADLINE: Monday 3 July 2017
CANCELLATION DEADLINE: Monday 10 July 2017
PLACES: 85 (lectures), 30 (hands-on sessions) (first come, first served)
REGISTRATION FEE: £70 for the lectures, £35 for each half-day hands-on
session (includes coffee/tea, but no lunch)
INFORMATION: Bert Overduin (bert.overduin at ed.ac.uk)

TO REGISTER: http://genomics.ed.ac.uk/services/gatk-best-
practices-variant-discovery

This workshop will focus on the core steps involved in calling variants
with the Broad’s Genome Analysis Toolkit, using the “Best Practices”
developed by the GATK team. You will learn why each step is essential to
the variant discovery process, what are the 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. In the course of this workshop,
we highlight key functionalities such as the GVCF workflow for joint
variant discovery in cohorts, RNAseq-specific processing, and somatic
variant discovery using MuTect2. We also preview capabilities of the
upcoming GATK version 4, including a new workflow for CNV discovery, and we
demonstrate the use of pipelining tools to assemble and execute GATK
workflows.

"Excellent opportunity to learn from world-renowned experts!" (April 2016)

INSTRUCTORS

GATK staff (The Broad Institute, Cambridge, MA, United States)

WORKSHOP FORMAT

The workshop is composed of one day of lectures (including many
opportunities for Q&A) and two optional days of hands-on training,
structured as follows:

Lectures (day 1): Rationale, theory and application of the GATK Best
Practices for Variant Discovery in high-throughput sequencing data.

Hands-on 1 (day 2 am): Germline variant discovery (SNPs + Indels)
Hands-on 2 (day 2 pm): Germline variant filtering (SNPs + Indels)

Hands-on 3 (day 3 am): Somatic variant discovery (SNPs + Indels + CNV)
Hands-on 4 (day 3 pm): Pipelining on the cloud with WDL

Please note that the lectures part is mandatory. It is not possible to
attend any of the hands-on sessions without attending the lectures.

In the three optional hands-on sessions focused on analysis, we walk
attendees through exercises that teach them how to manipulate the standard
data formats involved in variant discovery and how to apply GATK tools
appropriately to common use cases and data types. In the course of these
exercises, we demonstrate useful tips and tricks for interacting with GATK
and Picard tools, dealing with problems, and using third-party tools such
as Samtools, IGV, RStudio and RTG Tools.

In the optional hands-on session on pipelining, we walk attendees through
exercises that teach them to write workflow scripts using WDL, the Broad's
new Workflow Description Language, and to execute these workflows locally
as well as through publicly available cloud-based services.

Please note that this workshop is focused on human data analysis. The
majority of the materials presented applies equally to non-human data, and
we will address some questions regarding adaptations that are needed for
analysis of non-human data, but we will not go into much detail on those
points.

WHO SHOULD ATTEND

The lecture-based component of the workshop is aimed at a mixed audience of
people who are new to the topic of variant discovery or to GATK, seeking an
introductory course into the tools, or who are already GATK users seeking
to improve their understanding of and proficiency with the tools. Attendees
should already be familiar with the basic terms and concepts of genetics
and genomics.

The hands-on component is aimed at novice to intermediate users who are
seeking detailed guidance with GATK and related tools. Basic familiarity
with the command line environment is required.

Please note that for the hands-on sessions attendees will be expected to
bring their own laptops with software preinstalled (detailed instructions
will be posted two weeks before the workshop). Supported systems are Mac
and Unix/Linux systems. MS Windows is not supported.

COVERED TOPICS

Lectures

Introduction to variant discovery analysis and GATK Best Practices
Marking Duplicates
Indel Realignment
Base Recalibration
Variant Calling and Joint Genotyping
Filtering variants with VQSR
Genotype Refinement Workflow
Callset Evaluation
Somatic variant discovery with MuTect2
Preview of  CNV discovery with GATK4

Hands-on 1

Germline variant discovery (SNPs + Indels)

Hands-on 2

Germline variant filtering (SNPs + Indels)

Hands-on 3

Somatic variant discovery (SNPs + Indels + CNV)

Hands-on 4

Pipelining on the cloud with WDL

-- 
Bert Overduin, PhD
TRAINING AND OUTREACH BIOINFORMATICIAN
Bert.Overduin at ed.ac.uk
orcid.org/0000-0002-5281-8838

EDINBURGH GENOMICS
The University of Edinburgh
Ashworth Laboratories
The King's Buildings
Charlotte Auerbach Road
Edinburgh EH9 3FL
Scotland, United Kingdom

tel. +44(0)1316507403
http://genomics.ed.ac.uk
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