Affiliation:
1. Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota , 1352 Boyd Ave, Saint Paul, MN 55108 , USA
Abstract
Abstract
Advancements in massively parallel short-read sequencing technologies and the associated decreasing costs have led to large and diverse variant discovery efforts across species. However, processing high-throughput short-read sequencing data can be challenging with potential pitfalls and bioinformatics bottlenecks in generating reproducible results. Although a number of pipelines exist that address these challenges, these are often geared toward human or traditional model organism species and can be difficult to configure across institutions. Whole Animal Genome Sequencing (WAGS) is an open-source set of user-friendly, containerized pipelines designed to simplify the process of identifying germline short (SNP and indel) and structural variants (SVs) geared toward the veterinary community but adaptable to any species with a suitable reference genome. We present a description of the pipelines [adapted from the best practices of the Genome Analysis Toolkit (GATK)], along with benchmarking data from both the preprocessing and joint genotyping steps, consistent with a typical user workflow.
Funder
Agriculture and Food Research Initiative
NIH Special Emphasis Research Career Award
Publisher
Oxford University Press (OUP)
Subject
Genetics (clinical),Genetics,Molecular Biology
Cited by
4 articles.
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