Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.

ABSTRACT: Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-

SUBMITTER: David G 

PROVIDER: S-EPMC11018544 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature