ACGT, BSP and UP's GRI, team up to host the Genome Analysis ToolKit (GATK) workshop

The African Centre for Gene Technologies (ACGT) in conjunction with the Bioinformatics Service Platform (BSP) and UP’s Genomics Research Institute (GRI)  hosted a 5-day Genome Analysis ToolKit (GATK) Workshop between the 22-26 June 2015 at the  Centre for Bioinformatics and Computational Biology at UP .  The Toolkit was developed at the Broad Institute and was designed to analyse next-generation sequencing (NGS) data. Although it was initially developed for the analysis of human genomes, it has since been modified to handle and analyse data of non-model organisms by simply adapting and changing various parameters in the software.

A total of 23 delegates were trained at the workshop and this group was representative of three of the ACGT partner institutions (UP, ARC and WITS). Furthermore, attendees representing UNISA, Vaal University of Technology and North West University were also present.  The five day hands-on workshop was presented by Drs. Geraldine Van der Auwera, Laura Gauthier and Yossi Farjoun from The Broad Institute. The workshop focused on analysing human data, but also covered various strategies for adapting the Best Practices to the study of non-human and non-model organisms. Each day consisted of a lecture session in the morning and a hands-on session in the afternoon. In the afternoon session, the attendees had the opportunity to apply what they had learnt in the morning to real data through a variety of exercises as well as explore various useful tips and tricks to improve efficiency and deal with common problems. The topics were covered in the following order: (1) Introduction to high-throughput sequencing, experimental designs, QC, (2) Processing of sequence alignment data (i.e BAM files, incl. RNAseq), (3) Germline variant discovery + recalibration/filtering, (4) Somatic variant discovery + filtering and (5) Genotype refinement, variant manipulation & evaluation.

Overall, the workshop was well received and participants found it to be well presented and extremely useful and relevant to their research.

This workshop forms part of a series of open-source bioinformatics training workshops planned for 2015 that is being sponsored by the Bioinformatics Service Platform (BSP) and the ACGT. For further information on upcoming bioinformatics training events or to be added to our mailing list, visit the events page on the ACGT website or email Farhahna Allie (az.ca1569109146.ju@e1569109146illaf1569109146)

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