Our lab has been invited to host the next iteration of the Agricultural Genome to Phenome Initiative’s (AG2PI) workshop series this Thursday, Dec 2, 2021, from 12:00 to 2:00pm (MST). AG2PI is a United States Department of Agriculture’s National Institute of Food and Agriculture (USDA-NIFA) funded project whose focus is to integrate cross-discipline expertise in an effort to further our understanding of how the complex relationship between genotype, phenotype, and environmental factors influence crop and livestock production.

We are very excited to share our recent work on structural variant (SV) calling on population wide short-read sequencing data. Ryan, Murad, and Devin will walk through the steps required to perform SV calling as well as SV genotyping on a small salmon population, followed by our filtering and curation methods, and finally with a discussion on some possible avenues of analytic exploration using the SVs.

We hope via the workshop the participants will walk away with an appreciation for each of the steps in our SV calling pipeline such that they will be able to extract SVs from their own datasets with high confidence as well as perform their own analysis on their results. These steps will include the process of aligning sequencing data to a reference genome, identifying and excluding problematic regions in the sample data and the reference genome, perform SV calling and genotyping on each sample, and finally merge to produce a population level genotyped SV cohort.

In the analysis portion of the workshop we aim to walk the participants through various tools that allow for querying of a VCF file and how we can use those to find interesting and relevant evolutionary artifacts such as the loss of particular mobile elements in a species. We will also discuss how to perform phylogenetic analysis on extracted sequences of interest. Finally we will show participants the process of performing PCA on SV data to validate separation of subpopulations in the species population.

Attendance for this virtual workshop requires registration here

A recording will be available sometime in the future at www.ag2pi.org and we will also have a detailed written guide with tutorials on each of the steps available shortly.

~ Devin Burke CS Graduate Student Biofrontiers, CU Boulder