{"id":"https://openalex.org/W4413339515","doi":"https://doi.org/10.1186/s12859-025-06246-6","title":"SV-MeCa: an XGBoost-based meta-caller approach for structural variant calling from short-read data","display_name":"SV-MeCa: an XGBoost-based meta-caller approach for structural variant calling from short-read data","publication_year":2025,"publication_date":"2025-08-20","ids":{"openalex":"https://openalex.org/W4413339515","doi":"https://doi.org/10.1186/s12859-025-06246-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/40836322"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06246-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06246-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06246-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06246-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093524648","display_name":"Rudel Christian Nkouamedjo Fankep","orcid":"https://orcid.org/0000-0002-8751-8202"},"institutions":[{"id":"https://openalex.org/I4210153755","display_name":"University Hospital Cologne","ror":"https://ror.org/05mxhda18","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210153755"]},{"id":"https://openalex.org/I180923762","display_name":"University of Cologne","ror":"https://ror.org/00rcxh774","country_code":"DE","type":"education","lineage":["https://openalex.org/I180923762"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Rudel Christian Nkouamedjo Fankep","raw_affiliation_strings":["Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany"],"affiliations":[{"raw_affiliation_string":"Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany","institution_ids":["https://openalex.org/I4210153755","https://openalex.org/I180923762"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052523221","display_name":"Arda S\u00f6ylev","orcid":"https://orcid.org/0000-0003-2198-1920"},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Arda S\u00f6ylev","raw_affiliation_strings":["Center for Digital Medicine, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany","Institute for Medical Biometry and Bioinformatics, Heinrich Heine University D\u00fcsseldorf, Medical Faculty, D\u00fcsseldorf, Germany"],"affiliations":[{"raw_affiliation_string":"Center for Digital Medicine, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Institute for Medical Biometry and Bioinformatics, Heinrich Heine University D\u00fcsseldorf, Medical Faculty, D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093524645","display_name":"Anna-Lena Kobiela","orcid":"https://orcid.org/0009-0000-6391-1280"},"institutions":[{"id":"https://openalex.org/I4210153755","display_name":"University Hospital Cologne","ror":"https://ror.org/05mxhda18","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210153755"]},{"id":"https://openalex.org/I180923762","display_name":"University of Cologne","ror":"https://ror.org/00rcxh774","country_code":"DE","type":"education","lineage":["https://openalex.org/I180923762"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Anna-Lena Kobiela","raw_affiliation_strings":["Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany"],"affiliations":[{"raw_affiliation_string":"Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany","institution_ids":["https://openalex.org/I4210153755","https://openalex.org/I180923762"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071633943","display_name":"Jochen Blom","orcid":"https://orcid.org/0000-0001-6455-3622"},"institutions":[{"id":"https://openalex.org/I200763008","display_name":"University of Giessen","ror":"https://ror.org/033eqas34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200763008"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jochen Blom","raw_affiliation_strings":["Bioinformatics and Systems Biology, Justus Liebig University Gie\u00dfen, Gie\u00dfen, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, Justus Liebig University Gie\u00dfen, Gie\u00dfen, Germany","institution_ids":["https://openalex.org/I200763008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082895019","display_name":"Corinna Ernst","orcid":"https://orcid.org/0000-0001-7756-8815"},"institutions":[{"id":"https://openalex.org/I4210153755","display_name":"University Hospital Cologne","ror":"https://ror.org/05mxhda18","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210153755"]},{"id":"https://openalex.org/I180923762","display_name":"University of Cologne","ror":"https://ror.org/00rcxh774","country_code":"DE","type":"education","lineage":["https://openalex.org/I180923762"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Corinna Ernst","raw_affiliation_strings":["Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany. corinna.ernst@uk-koeln.de","Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany"],"affiliations":[{"raw_affiliation_string":"Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany. corinna.ernst@uk-koeln.de","institution_ids":[]},{"raw_affiliation_string":"Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany","institution_ids":["https://openalex.org/I4210153755","https://openalex.org/I180923762"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065415071","display_name":"Susanne Motameny","orcid":"https://orcid.org/0000-0003-1186-1108"},"institutions":[{"id":"https://openalex.org/I137533716","display_name":"German Sport University Cologne","ror":"https://ror.org/0189raq88","country_code":"DE","type":"education","lineage":["https://openalex.org/I137533716"]},{"id":"https://openalex.org/I180923762","display_name":"University of Cologne","ror":"https://ror.org/00rcxh774","country_code":"DE","type":"education","lineage":["https://openalex.org/I180923762"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Susanne Motameny","raw_affiliation_strings":["Cologne Center for Genomics, University of Cologne, Medical Faculty, Cologne, Germany. susanne.motameny@uni-koeln.de","West German Genome Center - Cologne, University of Cologne, Cologne, Germany. susanne.motameny@uni-koeln.de","Cologne Center for Genomics, University of Cologne, Medical Faculty, Cologne, Germany","West German Genome Center - Cologne, University of Cologne, Cologne, Germany"],"affiliations":[{"raw_affiliation_string":"Cologne Center for Genomics, University of Cologne, Medical Faculty, Cologne, Germany. susanne.motameny@uni-koeln.de","institution_ids":[]},{"raw_affiliation_string":"West German Genome Center - Cologne, University of Cologne, Cologne, Germany. susanne.motameny@uni-koeln.de","institution_ids":[]},{"raw_affiliation_string":"Cologne Center for Genomics, University of Cologne, Medical Faculty, Cologne, Germany","institution_ids":["https://openalex.org/I180923762"]},{"raw_affiliation_string":"West German Genome Center - Cologne, University of Cologne, Cologne, Germany","institution_ids":["https://openalex.org/I137533716"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5065415071"],"corresponding_institution_ids":["https://openalex.org/I137533716","https://openalex.org/I180923762"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.19294383,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"1","first_page":"218","last_page":"218"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9962000250816345,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9958000183105469,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5906978249549866},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39028817415237427},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37765946984291077},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37631869316101074},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24590855836868286}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5906978249549866},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39028817415237427},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37765946984291077},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37631869316101074},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24590855836868286}],"mesh":[{"descriptor_ui":"D000098404","descriptor_name":"Boosting Machine Learning Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098404","descriptor_name":"Boosting Machine Learning Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056914","descriptor_name":"Genomic Structural Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-025-06246-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06246-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06246-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40836322","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40836322","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12366149","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12366149","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:USBKOELN.ub.uni-koeln.de:80115","is_oa":false,"landing_page_url":"https://orcid.org/0000-0002-8751-8202>,","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:doaj.org/article:9f4f79064e6a457bad27e89028d1e6d4","is_oa":true,"landing_page_url":"https://doaj.org/article/9f4f79064e6a457bad27e89028d1e6d4","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-15 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06246-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06246-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06246-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320324811","display_name":"Universit\u00e4t zu K\u00f6ln","ror":"https://ror.org/00rcxh774"},{"id":"https://openalex.org/F4320327730","display_name":"Universit\u00e4tsklinikum K\u00f6ln","ror":"https://ror.org/05mxhda18"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413339515.pdf","grobid_xml":"https://content.openalex.org/works/W4413339515.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1544712555","https://openalex.org/W2065817684","https://openalex.org/W2083870688","https://openalex.org/W2111350087","https://openalex.org/W2119582595","https://openalex.org/W2146005104","https://openalex.org/W2154397429","https://openalex.org/W2235737683","https://openalex.org/W2289509647","https://openalex.org/W2295598076","https://openalex.org/W2582800429","https://openalex.org/W2605897695","https://openalex.org/W2620600112","https://openalex.org/W2792225186","https://openalex.org/W2948024819","https://openalex.org/W2949062400","https://openalex.org/W2951745476","https://openalex.org/W2972274962","https://openalex.org/W2990344913","https://openalex.org/W3034581902","https://openalex.org/W3113659825","https://openalex.org/W3130788486","https://openalex.org/W4210887696","https://openalex.org/W4225740064","https://openalex.org/W4307777744","https://openalex.org/W4313250582","https://openalex.org/W4379469205","https://openalex.org/W4391474878","https://openalex.org/W4402621858"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"SV-MeCa,":[0],"publicly":[1],"available":[2],"at":[3],"https://github.com/ccfboc-bioinformatics/SV-MeCa":[4],",":[5],"outperforms":[6],"existing":[7],"SV":[8],"meta-caller":[9],"approaches":[10],"by":[11],"taking":[12],"variant-specific":[13],"quality":[14],"measures":[15],"into":[16],"account.":[17],"Moreover,":[18],"due":[19],"to":[20,36],"the":[21,28],"XGBoost":[22],"prediction":[23],"probabilities":[24],"serving":[25],"as":[26],"scores,":[27],"output":[29],"of":[30,41],"SV-MeCa":[31],"can":[32],"be":[33],"continuously":[34],"adjusted":[35],"user":[37],"needs":[38],"in":[39],"terms":[40],"sensitivity":[42],"and":[43],"precision.":[44]},"counts_by_year":[],"updated_date":"2026-03-23T07:41:27.035349","created_date":"2025-10-10T00:00:00"}