{"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"],"raw_orcid":null,"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"],"raw_orcid":null,"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"],"raw_orcid":null,"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"],"raw_orcid":null,"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"],"raw_orcid":null,"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"],"raw_orcid":null,"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":0.22437324,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.7705000042915344,"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"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.7705000042915344,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.18279999494552612,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.021400000900030136,"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":true,"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/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","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":{"BACKGROUND:":[0],"Calling":[1],"structural":[2],"variants":[3],"(SVs),":[4],"i.e.,":[5,102],"genomic":[6],"alterations":[7],"of":[8,33,41,75,97,204,326,337],"\u226550bp,":[9],"from":[10,63,138],"whole":[11],"genome":[12],"short-read":[13],"data":[14,166],"remains":[15],"challenging,":[16],"as":[17,145,322],"existing":[18,303],"callers":[19,111],"are":[20,45,136],"known":[21],"to":[22,88,95,182,186,201,233,258,282,316,332],"lack":[23],"accuracy":[24],"and":[25,73,112,116,143,206,245,279,339],"robustness.":[26],"Therefore,":[27],"meta-caller":[28,58,210,305],"approaches":[29,211,306],"combining":[30],"the":[31,55,130,162,169,197,223,253,317,324],"results":[32],"multiple":[34],"standalone":[35,109,140],"tools":[36,76],"in":[37,129,171,219,335],"a":[38,85,120,172,180],"consensus":[39,78,91],"set":[40],"reported":[42],"SV":[43,57,79,92,110,164,184,217,304],"calls,":[44,101,190],"widely":[46],"used.":[47],"Here,":[48],"SV-MeCa":[49,83,106,176,205,251,284,327],"(Structural":[50],"Variant":[51],"Meta-Caller)":[52],"is":[53],"presented,":[54],"first":[56],"incorporating":[59],"variant-specific":[60,309],"quality":[61,134,310],"metrics":[62],"individual":[64],"VCF":[65,122,141],"outputs,":[66],"rather":[67],"than":[68],"relying":[69],"solely":[70],"on":[71,161,215,241,247,268,275],"number":[72],"combination":[74],"supporting":[77],"calls.":[80],"In":[81],"addition,":[82],"offers":[84],"suitable":[86],"score":[87],"rank":[89],"obtained":[90],"calls":[93,118,185,218],"according":[94,200],"evidence":[96],"representing":[98],"true":[99,188],"positive":[100,189],"real-world":[103],"variants.":[104],"RESULTS:":[105],"applies":[107],"seven":[108],"merges":[113],"resulting":[114],"deletion":[115],"insertion":[117],"into":[119,312],"union":[121],"file":[123],"using":[124],"SURVIVOR.":[125],"For":[126],"each":[127],"entry":[128],"SURVIVOR-generated":[131],"consensus,":[132],"caller-specific":[133],"measures":[135,311],"extracted":[137],"corresponding":[139],"files,":[142],"serve":[144],"input":[146],"for":[147,195,243,249,270,277,290],"an":[148],"either":[149],"deletion-":[150],"or":[151],"insertion-specific":[152],"XGBoost":[153,177,318],"decision":[154],"tree":[155],"classifier,":[156],"which":[157,191,238],"was":[158,285],"previously":[159,208],"trained":[160],"HG002":[163],"benchmark":[165],"provided":[167],"by":[168,222,288,307],"Genome":[170,225],"Bottle":[173],"consortium.":[174],"The":[175],"models":[178],"assign":[179],"probability":[181],"(consensus)":[183],"represent":[187],"can":[192,328],"be":[193,329],"used":[194],"ranking":[196],"final":[198],"output":[199,325],"evidence.":[202],"Performance":[203],"four":[207],"published":[209],"were":[212,239],"evaluated":[213],"based":[214],"autosomal":[216],"samples":[220],"curated":[221],"Human":[224],"Structural":[226],"Variation":[227],"Consortium,":[228],"Phase":[229],"2.":[230],"With":[231,256],"regard":[232,257,281],"F[Formula:":[234],"see":[235],"text]":[236],"scores,":[237,323],"0.58":[240],"average":[242,248,269,276],"deletions":[244,291],"0.42":[246],"insertions,":[250],"outperformed":[252,286],"other":[254],"meta-callers.":[255],"precision,":[259],"only":[260],"ConsensuSV":[261],"achieved":[262],"higher":[263],"values":[264],"(0.97":[265],"versus":[266,273,293],"0.64":[267],"deletions,":[271],"0.75":[272],"0.53":[274],"insertions),":[278],"with":[280],"recall,":[283],"exclusively":[287],"Meta-SV":[289],"(0.55":[292],"0.53).":[294],"CONCLUSIONS:":[295],"SV-MeCa,":[296],"publicly":[297],"available":[298],"at":[299],"https://github.com/ccfboc-bioinformatics/SV-MeCa":[300],",":[301],"outperforms":[302],"taking":[308],"account.":[313],"Moreover,":[314],"due":[315],"prediction":[319],"probabilities":[320],"serving":[321],"continuously":[330],"adjusted":[331],"user":[333],"needs":[334],"terms":[336],"sensitivity":[338],"precision.":[340]},"counts_by_year":[],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
