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Keywords: Variant calling 

and

Authors: Coddington, Paul (orcid: 00...  or Price, Gareth (orcid: 0000-...  or Nisselle, Amy (orcid: 0000-... 

WORKSHOP: Variant calling in humans, animals and plants with Galaxy

This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.

Variant calling in polyploid organisms, including humans, plants and animals, can help determine single...

Keywords: Variant calling, Genetic Variation Analysis, SNP annotation

WORKSHOP: Variant calling in humans, animals and plants with Galaxy https://dresa.org.au/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy-767f1816-1c06-478c-adf4-90b3b2d32a9c This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021. Variant calling in polyploid organisms, including humans, plants and animals, can help determine single or multi-variant contributors to a phenotype. Further, sexual reproduction (as compared to asexual) combines variants in a novel manner; this can be used to determine previously unknown variant - phenotype combinations but also to track lineage and lineage associated traits (GWAS studies), that all rely on highly accurate variant calling. The ability to confidently call variants in polyploid organisms is highly dependent on the balance between the frequency of variant observations against the background of non-variant observations, and even further compounded when one considers multi-variant positions within the genome. These are some of the challenges that will be explored in the workshop. In this online workshop we focused on the tools and workflows available for variant calling in polyploid organisms in Galaxy Australia. The workshop provided opportunities for hands-on experience using Freebayes for variant calling and SnpEff and GEMINI for variant annotation. The workshop made use of data from a case study on diagnosing a genetic disease however the tools and workflows are equally applicable to other polyploid organisms and biological questions. Access to all of the tools covered in this workshop was via Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event.   Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Schedule (PDF): schedule for the workshop Variant calling - humans, animals, plants - slides (PPTX and PDF): slides used in the workshop   Materials shared elsewhere: The tutorial used in this workshop is available via the Galaxy Training Network. Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning, 2021 Exome sequencing data analysis for diagnosing a genetic disease (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html Online; accessed 25 May 2021 Melissa Burke (melissa@biocommons.org.au) Variant calling, Genetic Variation Analysis, SNP annotation
WEBINAR: Variant interpretation: from the clinic to the lab… and back again

This record collates training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Variant interpretation: from the clinic to the lab… and back again’. This webinar took place on 7 December 2022.

Event description 

The use of genomic testing is increasing rapidly as...

Keywords: Clinical genomics, Variant interpretation, Variant curation, Continuing Professional Development, Professional Development, Bioinformatics, Genomics, Variant calling

WEBINAR: Variant interpretation: from the clinic to the lab… and back again https://dresa.org.au/materials/webinar-variant-interpretation-from-the-clinic-to-the-lab-and-back-again-5c6aed91-24cd-4314-9638-5e60d51e1af1 This record collates training materials associated with the Australian BioCommons/Melbourne Genomics webinar ‘Variant interpretation: from the clinic to the lab… and back again’. This webinar took place on 7 December 2022. Event description  The use of genomic testing is increasing rapidly as the cost of genome sequencing decreases. Many areas of the health workforce are upskilling in genomics to help meet the increased demand. From clinicians learning how to use the right test, for the right patient, at the right time, to medical scientists learning how to interpret and classify variants, and data scientists to learning how to better create and continuously refine the pipelines and software to handle and curate big data. In this webinar, we’ll hear from two people working at the coalface of variant interpretation – one in a diagnostic laboratory and the other in a cancer research laboratory. Naomi Baker is Medical Scientist at Victorian Clinical Genetics Services. She helps process hundreds of genomic tests per year to find the variants that cause rare diseases. She’ll explain the clinical variant interpretation processes she uses, the pipelines, professions and people involved. Joep Vissers is a Curation Team Leader, at the University of Melbourne Centre for Cancer Research, Department of Clinical Pathology. Joep, who also teaches cancer biology at the University, will describe how he uses variant interpretation in his work at the research/clinical interface, and the shift in mindset required when working with data for these different purposes. Amy Nisselle, Genomics Workforce Lead at Melbourne Genomics, will then briefly outline some of the education programs available in clinical variant interpretation. This webinar is co-presented by Australian BioCommons and Melbourne Genomics Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event. Files and materials included in this record: Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc. Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file. Variant interpretation from the clinic to the lab and back again.pdf: A PDF copy of the slides presented during the webinar. Materials shared elsewhere: A recording of this webinar is available on the Australian BioCommons YouTube Channel: https://youtu.be/wLMhwIiK8Lw Melissa Burke (melissa@biocommons.org.au) Clinical genomics, Variant interpretation, Variant curation, Continuing Professional Development, Professional Development, Bioinformatics, Genomics, Variant calling