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 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

Scientific topics: Genetic variation

Keywords: Variant calling

Licence: Creative Commons Attribution 4.0

Doi: 10.5281/zenodo.5076667

WORKSHOP: Variant calling in humans, animals and plants with Galaxy http://tess.elixir-uk.org/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy This Zenodo 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. Genetic variation Variant calling