NGS - Genome Variant analysis – Variant calling (3 of 5)
Channel: SIB - Swiss Institute of Bioinformatics
Date: 18/10/2023

The video was recorded live during the SIB course “NGS - Genome Variant analysis” streamed on 05-06 September 2023. 

Target audience: This course is intended for life scientists who are already familiar with general concepts of NGS technologies and want to expand their knowledge and skills on variant analysis. 

Speaker: Dr. Geert van Geest, SIB Swiss Institute of Bioinformatics 

The course materials can be found in the dedicated GitHub page: https://sib-swiss.github.io/NGS-variants-training/ . 

Learning outcomes: 

Describe how variant information is stored in a variant call format (.vcf) file 

Describe the ‘missing genotype problem’ when calling variants of multiple samples, and the different methods on how this can be solved 

Perform basic calculations regarding the genotype likelihood of individual variants 

Follow gatk best practices workflow to perform a variant analysis by: 

Calling variants with gatk HaplotypeCaller 

Combining multiple vcf files into a single vcf file 

Any questions about this talk? Contact: Geert van Geest, geert.vangeest@sib.swiss 

This video is available under the creative commons license CC-BY-4.0