class: center, middle, inverse, title-slide # .huge[VCF-DART] ## (VCF Diagnostic Annotation and Reporting Tool) ###
Dr Miles Benton
Senior Scientist Bioinformatics, ESR
### (QRW Bioinformatics - 30
th
-31
st
August 2018) --- class: middle # .center[Advocate for reproducible research...] ## .center[Where possible my presentations and code are available online] <br /> <p> .center[ <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;"/> ] </p> <br /> .center[[sirselim.github.io/presentations](http://sirselim.github.io/presentations)] --- class: middle inverse <p> .center[<img src="images/jamie.jpg" style="width: 40%; margin-right: 1%; margin-top: -0.5em; border: 3px solid white;"/>] </p> --- class: middle inverse # ESR (2<sup>nd</sup> July 2018 - ) ## Wellington (Porirua), NZ ### <span style="color:#3498DB">Senior Scientist Bioinformatics and Data Science</span> --- layout: false background-image: url("images/desk.jpg") background-size: cover --- class: middle inverse # QUT (Feburary 2014 - June 2018) ## Brisbane (QLD), Australia ### <span style="color:#3498DB">PostDoc Research Fellow</span> --- layout: false background-image: url("images/proton2.jpg") background-size: cover --- class: middle # Diagnostics Lab .large[Gene panel and Exome Sequencing (NATA accredited - neurological disorders)] <br> ## Sanger -> Gene panel -> Exome * used to manually work through 30-60K rows of data in Excel! * could take 4-8 weeks to identify and validate variant(s) --- class: middle inverse # VCF-DART - what it's not... It is **NOT** a variant calling and quality control pipeline ... it's about data --- # Overview <p> .center[<img src="images/Pipeline_flowchart_v2.png" style="width: 95%; margin-right: 1%; margin-top: -0.5em; border: 3px solid white;"/>] </p> --- # Variant tiers <p> .center[<img src="images/tiers.png" style="width: 70%; margin-right: 1%; margin-top: -0.5em; border: 3px solid white;"/>] </p> --- class: middle inverse # "Module 1" - VCF-DART --- layout: false background-image: url("images/vcfdart_1.png") background-size: contain --- layout: false background-image: url("images/vcfdart_2.png") background-size: contain --- class: middle # Runtime .huge[30-50K variants (avg Proton exome VCF):] - 6-10 mins (24 core 256GB RAM) - 17-23 mins (4 core 12GB RAM) --- class: middle inverse # "Module 2" - VCF-DART Viewer --- class: middle center .huge[[...live demonstration...](https://43.240.99.48/sample-apps/WES_ShinyDiscover/)] <br> .huge[**?**] --- layout: false background-image: url("images/backup_1.png") background-size: contain --- layout: false background-image: url("images/backup_2.png") background-size: contain --- layout: false background-image: url("images/backup_3.png") background-size: contain --- layout: false background-image: url("images/backup_4.png") background-size: contain --- layout: false background-image: url("images/backup_5.png") background-size: contain --- layout: false background-image: url("images/backup_6.png") background-size: contain --- class: <p> .center[<img src="images/nectarcloud.png" style="width: 70%; margin-right: 1%; margin-top: -0.5em; border: 3px solid white;"/>] </p> Spun up VM to give reviewers a chance to ~~break~~ test things. * using 6 public exomes (1000G) <br> -- .large[**Allocated VM:**] * Ubuntu 18.08 * 4 cores * 12GB RAM * 30GB root * 120GB ephemeral disk -- <br> ...so it can scale down to quite reasonable specs... --- class: middle ## VCF-DART in the lab * now can have a short list of variants in <span style="color:#3498DB">**1 day**</span> * validation in <span style="color:#3498DB">**<2 weeks**</span> ## Summary * open source * modular (tools and databases) * scalable (laptops -> servers) * easy to deploy and use --- class: middle inverse # to-do * ~~submit~~ manuscript - out for review (Genetics in Medicine) * release to the wild (anyone interested can help out) * finish implementing ClinGen links * option for GnomAD-beta * refactoring main code base (bpipe) * complete docker version * continue developing documentation! * work with clinicians to further develop and refine --- class: top # 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) Sam Beardman QRISCloud / Nectar --- class: middle inverse <p> .huge[.center[<b>Thank you!</b>]] <br> </p>