.huge[VCF-DART]

# .huge[VCF-DART]
## A Customisable Analysis Pipeline for the Identification of Clinically Relevant Genetic Variants in Next Generation Sequencing Data
### <div class="line-block"><a href="http://sirselim.github.io/">Dr Miles Benton</a> 
Senior Scientist Bioinformatics 
Human Genomics, Institute of Environmental Science and Research (ESR) 
 
.large[HGSA Wellington, 3rd-6th August 2019] 
 
 
.center[<img src="images/ESR_SFC_logo.png" style="width: 25%; border: 3px solid white;"/>]</div>

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# .center[Advocate for reproducible research...]

## .center[Where possible my presentations and code are available online]

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<img src="images/github_logo.png" style="width: 520px; margin-right: 1%; margin-top: 1.5em;"/>
<img src="images/sirselim_qrcode.png" style="width: 202px; margin-right: 1%; margin-top: 1.5em;"/>
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.center[[sirselim.github.io/presentations](http://sirselim.github.io/presentations)]
  
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# QUT (February 2014 - June 2018)

## Brisbane (QLD), Australia

### PostDoc Research Fellow

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# Diagnostics Lab

## Sanger -> Gene panel -> Exome

* move to WES -> increase in variants
* manual approach through 30-60K rows of data in Excel
* increased time to identify and validate variant(s)

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# VCF-DART - what it's not...

It is **NOT** a variant calling and quality control pipeline

... it's about data

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# Overview

.center[<img src="images/Pipeline_flowchart_v2.png" style="width: 95%; margin-right: 1%; margin-top: -0.5em; border: 3px solid white;"/>]

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# Variant tiers

.center[<img src="images/tiers.png" style="width: 70%; margin-right: 1%; margin-top: -0.5em; border: 3px solid white;"/>]

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# "Module 1" - VCF-DART

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# Run-time

- 6-10 mins (24 core 256GB RAM)
  - 17-23 mins (4 core 12GB RAM)

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# "Module 2" - VCF-DART Viewer

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.center[<img src="images/nectarcloud.png" style="width: 70%; margin-right: 1%; margin-top: -0.5em; border: 3px solid white;"/>]

Spun up VM to give reviewers a chance to ~~break~~ test things.

* using 6 public exomes (1000G)

* Ubuntu 18.08
* 4 cores
* 12GB RAM
* 30GB root
* 120GB ephemeral disk

...so it can scale down to quite reasonable specs...

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## VCF-DART in the lab

* much quicker time to variant shortlist and curation 
* can get to validation sooner (if required)
* meaning report delivered faster

## Summary

* open source
* modular (tools and databases)
* scalable (laptops -> servers)
* easy to deploy and use [soon to become easier]
* versioning

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## Current state of play

* exciting times!

* cancer genomics - Auckland University (Prof Cristin Print), Genomics Aotearoa

* merging 'pipelines' to offer a flexible, unified and freely distributed system across NZ

* accreditation

.center[
<img src="images/UoA.png" style="width: 272px; margin-right: 1%; margin-top: 1.5em; border: #FFFFFF 3.5px outset;"/>
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## Availability / Deployment

.center[
<img src="images/github.jpg" style="width: 200px; margin-right: 2%;"/>
<img src="images/aws.png" style="width: 215px; margin-right: 2%;"/>
<img src="images/singularity-logo.svg" style="width: 135px; margin-right: 2%; margin-left: 2%;"/>
<img src="images/NESI-logo.jpg" style="width: 300px; margin-right: 2%;"/>
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# to-do

* &#10004; ~~submit~~ manuscript - accepted (The Journal of Molecular Diagnostics) 
* &#10004; [release to the wild - GitHub (anyone interested can help out)](https://github.com/sirselim/WES_ShinyDiscover)
* finish implementing ClinGen & ClinVar links
* option for GnomAD-beta
* refactoring main code base (snakemake)
* complete docker/singularity version
* continue developing documentation!
* work with clinicians to further develop and refine

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# acknowledgements

<div id="images">
 <a href="http://xyz.com/hello">
 <img src="images/robert.jpg" width="180px" height="250px">
 <div class="caption">Dr Robert Smith (QUT)</div>
 </a>
 <a href="http://xyz.com/hi">
 <img src="images/donia.jpg" width="180px" height="250px"> 
 <div class="caption">Dr Donia Macartney-Coxson (ESR)</div>
 </a>
</div>

Craig Windell (QUT)

QUT lab group
]]

Dr Ben Curran (UoA)

Wellington Regional Genetics Lab

QRISCloud / Nectar 
]]

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