{"entity": "researcher", "timestamp": "2026-05-15T01:13:56.988Z", "family": "Layer", "given": "Ryan", "initials": "R", "orcid": "0000-0002-5823-3232", "affiliations": ["BioFrontiers Institute, University of Colorado, Boulder, CO, USA.", "Department of Computer Science, University of Colorado, Boulder, CO, USA."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/e448323eee2b4098a3fc8b7e4e610524.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/e448323eee2b4098a3fc8b7e4e610524"}}, "publications": [{"entity": "publication", "iuid": "1d736b8b72eb494b9bb389cec88fafc6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d736b8b72eb494b9bb389cec88fafc6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d736b8b72eb494b9bb389cec88fafc6"}}, "title": "Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.", "authors": [{"family": "David", "given": "Gabriel", "initials": "G", "orcid": "0009-0007-2935-3335", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b3c0232a812453cb58532f946233fad.json"}}, {"family": "Bertolotti", "given": "Alicia", "initials": "A"}, {"family": "Layer", "given": "Ryan", "initials": "R", "orcid": "0000-0002-5823-3232", "researcher": {"href": "https://publications.scilifelab.se/researcher/e448323eee2b4098a3fc8b7e4e610524.json"}}, {"family": "Scofield", "given": "Douglas", "initials": "D"}, {"family": "Hayward", "given": "Alexander", "initials": "A", "orcid": "0000-0001-7413-718X", "researcher": {"href": "https://publications.scilifelab.se/researcher/c5472a9b21fa405eaef0dba5323746ad.json"}}, {"family": "Baril", "given": "Tobias", "initials": "T", "orcid": "0000-0002-5936-7531", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf3dffb6823e4a56af5d7f5760a73bd4.json"}}, {"family": "Burnett", "given": "Hamish A", "initials": "HA"}, {"family": "Gudmunds", "given": "Erik", "initials": "E"}, {"family": "Jensen", "given": "Henrik", "initials": "H", "orcid": "0000-0001-7804-1564", "researcher": {"href": "https://publications.scilifelab.se/researcher/27e3fe8ca67c4bfea44b8bff1f996f8c.json"}}, {"family": "Husby", "given": "Arild", "initials": "A", "orcid": "0000-0003-1911-8351", "researcher": {"href": "https://publications.scilifelab.se/researcher/a30bcb02f8a44229815afcf33cd62d23.json"}}], "type": "journal article", "published": "2024-04-02", "journal": {"title": "Genome Biol Evol", "issn": "1759-6653", "volume": "16", "issue": "4", "issn-l": "1759-6653"}, "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-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.", "doi": "10.1093/gbe/evae049", "pmid": "38489588", "labels": {"Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11018544"}, {"db": "pii", "key": "7630036"}], "notes": [], "created": "2024-11-12T19:38:46.847Z", "modified": "2024-11-25T10:24:06.035Z"}]}