AG2PI Workshop #9 - Structural Variant Detection in Animal Populations

AG2PI Workshop #9 - Structural Variant Detection in Animal Populations
December 2, 2021

In this workshop, Ryan Layer and Murad Chowdhury will cover the basics of Structural Variant (SV) calling with Illumina short-read sequencing data. We will focus on the additional steps required for calling SVs in non-human populations with lower quality reference genomes and fewer genome annotation resources. We will go over each step of the SV calling pipeline, including alignment of DNA sequencing data to a reference genome, calling SVs, filtering methods for false-positive SV calls, and the visualization of SV genomic loci for manual curation call sets.

The workshop will include tutorials on using standard command-line tools to take your sequencing data (fastq) through obtaining SV calls in the Variant Call Format (VCF). We will also show how to combine these steps to create reproducible data pipelines using the Snakemake workflow management system. After this workshop, attendees will understand better how to call and curate SVs in their target populations.

Attendees should have a basic knowledge of Unix command line navigation. AG2PI previously hosted a workshop series dedicated to this: Workshop #7: Unix Skills and Git Skills. Recordings of these workshops are available at: https://www.ag2pi.org/workshops-and-activities/workshop-2021-09/