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

Price, Gareth

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

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Event metadata.pdf
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Index of training materials.pdf
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Schedule.pdf
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Variant calling - humans, animals, plants - slides.pdf
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Variant calling - humans, animals, plants - slides.pptx
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  • 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

  • Wellcome Genome Campus, 2021. Achievements and uniqueness. https://www.wellcomegenomecampus.org/scienceandinnovation/achievements-uniqueness/ Online; accessed 25 May 2021.

  • Miller, N.A., Farrow, E.G., Gibson, M. et al. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Med 7, 100 (2015). https://doi.org/10.1186/s13073-015-0221-8

  • Illumina. 2017. An introduction to Next-Generation Sequencing Technology. https://www.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf Online; accessed 25 May 2021.

  • Mardis, E. R. 2012. Applying next-generation sequencing to pancreatic cancer treatment. Nat. Rev. Gastroenterol. Hepatol. doi:10.1038/nrgastro.2012.126

  • Jose Carbonell-Caballero, Roberto Alonso, Victoria Ibañez, Javier Terol, Manuel Talon, Joaquin Dopazo, A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus, Molecular Biology and Evolution, Volume 32, Issue 8, August 2015, Pages 2015–2035, https://doi.org/10.1093/molbev/msv082

  • Freebayes 2021. freebayes, a haplotype-based variant detector: user manual and guide. Version 13 February 2021. https://github.com/freebayes/freebayes/blob/master/README.md Online, accessed 25 May 2021

  • Kulawiec, M., Owens, K. & Singh, K. 2009. mtDNA G10398A variant in African-American women with breast cancer provides resistance to apoptosis and promotes metastasis in mice. J Hum Genet 54, 647–654. https://doi.org/10.1038/jhg.2009.89

  • Wikipedia. 2021. Pile up format. https://en.wikipedia.org/wiki/Pileup_format Online, accessed 25 May 2021.

  • The Pevsner Laboratory. SNP Trio. http://pevsnerlab.kennedykrieger.org/php/?q=node/85 Online, accessed 25 May 2021.

  • Richards, S., Aziz, N., Bale, S. et al. 2015. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17, 405–423. https://doi.org/10.1038/gim.2015.30

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