BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260407T211854Z UID:3094b0fe-00ad-4cfa-9cd6-cc83a1ccc4ba DTSTART:20210525T030000Z DTEND:20210525T070000Z DESCRIPTION:Variant calling in polyploid organisms\, including humans\, pla nts and animals\, can help determine single or multi-variant contributors to a phenotype. Further\, sexual reproduction (as compared to asexual) com bines variants in a novel manner\; this can be used to determine previousl y unknown variant - phenotype combinations but also to track lineage and l ineage associated traits (GWAS studies)\, that all rely on highly accurate variant calling. The ability to confidently call variants in polyploid or ganisms is highly dependent on the balance between the frequency of varian t observations against the background of non-variant observations\, and ev en further compounded when one considers multi-variant positions within th e genome. These are some of the challenges that will be explored in the wo rkshop.\n\nIn this online workshop we focus on the tools and workflows ava ilable for variant calling in polyploid organisms in Galaxy Australia. Dur ing the workshop you will get hands-on experience using Freebayes for vari ant calling and SnpEff and GEMINI for variant annotation. The workshop mak es use of data from a case study on diagnosing a genetic disease however t he tools and workflows are equally applicable to other polyploid organisms and biological questions.\n\nAccess to all of the tools covered in this w orkshop is via [Galaxy Australia](https://usegalaxy.org.au/)\, an online p latform for biological research that allows people to use computational da ta analysis tools and workflows without the need for programming experienc e.\n\nYou may also be interested in our workshops on variant calling in vi ruses and bacteria. See our[ events page](https://www.biocommons.org.au/ev ents) for more information.\n\n**Date/time**: 1-5pm AEST\, Tuesday 25 May 2021\n\n**Lead Trainers:** Dr Gareth Price\, Dr Igor Makunin\, QCIF Bioin formatics.\n\n**Learning outcomes**\n\nThe materials to be covered in the workshop are freely available via the [Galaxy Training Network](https://tr aining.galaxyproject.org/training-material/topics/variant-analysis/tutoria ls/exome-seq/tutorial.html).\n\nBy the end of the workshop you should be a ble to:\n\n- Identify genetic variants in samples based on exome sequencin g data\n- Identify causative variants associated with a given phenotype\n- Apply Freebayes for variant calling\n- Apply SnpEff and GEMINI for varian t annotation\n\nThe workshop will NOT provide an introduction to the basic s of Galaxy or the use of Galaxy for sequencing analysis (e.g. quality con trol and mapping). If you would like to learn about these topics there are several tutorials available via the [Galaxy Training Network](https://tra ining.galaxyproject.org/training-material/).\n\n**Who the workshop is for* *\n\nThis workshop is for Australian researchers who have or will work on variant calling in polyploid organisms as part of their projects.\n\nTo ge t the most out of the workshops you must be familiar with the concepts of variant calling and have some experience with the basics of using Galaxy A ustralia such as setting up a history\, uploading data and running tools. No programming experience is required.\n\nYou will be required to watch an introductory webinar (either live or recorded) that will provide an overv iew of Galaxy Australia and introduce key functionalities of the service. If you are new to Galaxy we recommend that you work through the following tutorials in advance: [A short introduction to Galaxy](https://training.ga laxyproject.org/training-material/topics/introduction/tutorials/galaxy-int ro-short/tutorial.html) and [Galaxy 101 for Everyone](https://training.gal axyproject.org/training-material/topics/introduction/tutorials/galaxy-intr o-101-everyone/tutorial.html).\n\n**How to apply**\n\nThis workshop is fre e but participation is subject to application with selection. **_Applicati ons close at 5pm AEST Wednesday 12 May 2021._**\n\nYou must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered.\n\nApplications will be reviewed by the organising committee and all applicants will be informe d of the status of their application (successful\, waiting list\, unsucces sful) by Friday 14 May 2021. Successful applicants will be provided with a Zoom meeting link closer to the date.\n\n**[Apply here](https://biocommon s-variants-polyploid.eventbrite.com.au/)**\n\nThis workshop is presented b y the [Australian BioCommons](https://www.biocommons.org.au/) and [Queensl and Cyber Infrastructure Foundation (QCIF)](https://www.qcif.edu.au/) with the assistance of a network of facilitators from the national [Bioinforma tics Training Cooperative](https://www.biocommons.org.au/training-cooperat ive) and [Galaxy Australia](https://usegalaxy.org.au/).\n\nThis event is p art of a series of [bioinformatics training events](https://www.biocommons .org.au/events). If you'd like to hear when registrations open for other e vents\, please [subscribe](https://www.biocommons.org.au/subscribe) to Aus tralian BioCommons. SUMMARY:WORKSHOP: Variant calling in humans\, animals and plants with Galax y URL;VALUE=URI:https://www.biocommons.org.au/events/variants-polyploid END:VEVENT END:VCALENDAR