{"id":"https://openalex.org/W2602156049","doi":"https://doi.org/10.1186/s12859-017-1537-8","title":"GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data","display_name":"GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data","publication_year":2017,"publication_date":"2017-03-01","ids":{"openalex":"https://openalex.org/W2602156049","doi":"https://doi.org/10.1186/s12859-017-1537-8","mag":"2602156049","pmid":"https://pubmed.ncbi.nlm.nih.gov/28361668"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1537-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1537-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1537-8","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/track/pdf/10.1186/s12859-017-1537-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037048847","display_name":"Simona De Summa","orcid":"https://orcid.org/0000-0001-9607-3754"},"institutions":[{"id":"https://openalex.org/I4210131058","display_name":"Istituto Tumori Bari","ror":"https://ror.org/03jxkz251","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210099368","https://openalex.org/I4210117053","https://openalex.org/I4210131058","https://openalex.org/I4210153126"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simona De Summa","raw_affiliation_strings":["IRCCS-Istituto Tumori \"Giovanni Paolo II\", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy","IRCCS-Istituto Tumori \u201cGiovanni Paolo II\u201d, Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IRCCS-Istituto Tumori \"Giovanni Paolo II\", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy","institution_ids":[]},{"raw_affiliation_string":"IRCCS-Istituto Tumori \u201cGiovanni Paolo II\u201d, Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy","institution_ids":["https://openalex.org/I4210131058"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037463942","display_name":"Giovanni Malerba","orcid":"https://orcid.org/0000-0001-8705-8560"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Giovanni Malerba","raw_affiliation_strings":["Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy. giovanni.malerba@univr.it","Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy. giovanni.malerba@univr.it","institution_ids":[]},{"raw_affiliation_string":"Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110210154","display_name":"Rosamaria Pinto","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131058","display_name":"Istituto Tumori Bari","ror":"https://ror.org/03jxkz251","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210099368","https://openalex.org/I4210117053","https://openalex.org/I4210131058","https://openalex.org/I4210153126"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Rosamaria Pinto","raw_affiliation_strings":["IRCCS-Istituto Tumori \"Giovanni Paolo II\", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy","IRCCS-Istituto Tumori \u201cGiovanni Paolo II\u201d, Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IRCCS-Istituto Tumori \"Giovanni Paolo II\", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy","institution_ids":[]},{"raw_affiliation_string":"IRCCS-Istituto Tumori \u201cGiovanni Paolo II\u201d, Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy","institution_ids":["https://openalex.org/I4210131058"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085588754","display_name":"Antonio Mori","orcid":"https://orcid.org/0000-0003-2845-5931"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Antonio Mori","raw_affiliation_strings":["Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010074793","display_name":"Vladan Mijatovic","orcid":null},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Vladan Mijatovic","raw_affiliation_strings":["Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014032423","display_name":"Stefania Tommasi","orcid":"https://orcid.org/0000-0002-2157-2978"},"institutions":[{"id":"https://openalex.org/I4210131058","display_name":"Istituto Tumori Bari","ror":"https://ror.org/03jxkz251","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210099368","https://openalex.org/I4210117053","https://openalex.org/I4210131058","https://openalex.org/I4210153126"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefania Tommasi","raw_affiliation_strings":["IRCCS-Istituto Tumori \"Giovanni Paolo II\", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy","IRCCS-Istituto Tumori \u201cGiovanni Paolo II\u201d, Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IRCCS-Istituto Tumori \"Giovanni Paolo II\", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy","institution_ids":[]},{"raw_affiliation_string":"IRCCS-Istituto Tumori \u201cGiovanni Paolo II\u201d, Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy","institution_ids":["https://openalex.org/I4210131058"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037463942"],"corresponding_institution_ids":["https://openalex.org/I119439378"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":7.6096,"has_fulltext":true,"cited_by_count":122,"citation_normalized_percentile":{"value":0.97453365,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"18","issue":"S5","first_page":"119","last_page":"119"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.871999979019165,"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":0.871999979019165,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.07190000265836716,"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":0.014399999752640724,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7178812623023987},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6483944058418274},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5757738947868347},{"id":"https://openalex.org/keywords/sanger-sequencing","display_name":"Sanger sequencing","score":0.5224241614341736},{"id":"https://openalex.org/keywords/cutoff","display_name":"Cutoff","score":0.48182860016822815},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.46753594279289246},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.45461520552635193},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4138375222682953},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3889541029930115},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37191489338874817},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3595808744430542},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33581697940826416},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29811230301856995},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20410028100013733},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1521436870098114}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7178812623023987},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6483944058418274},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5757738947868347},{"id":"https://openalex.org/C76818968","wikidata":"https://www.wikidata.org/wiki/Q181940","display_name":"Sanger sequencing","level":4,"score":0.5224241614341736},{"id":"https://openalex.org/C2778217198","wikidata":"https://www.wikidata.org/wiki/Q556977","display_name":"Cutoff","level":2,"score":0.48182860016822815},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46753594279289246},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.45461520552635193},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4138375222682953},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3889541029930115},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37191489338874817},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3595808744430542},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33581697940826416},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29811230301856995},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20410028100013733},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1521436870098114},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","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":"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D059472","descriptor_name":"Exome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059472","descriptor_name":"Exome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059472","descriptor_name":"Exome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-017-1537-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1537-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1537-8","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:28361668","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28361668","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:5374681","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5374681","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1537-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1537-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1537-8","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":[{"id":"https://metadata.un.org/sdg/10","score":0.6399999856948853,"display_name":"Reduced inequalities"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321781","display_name":"Ministero della Salute","ror":"https://ror.org/00789fa95"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2602156049.pdf","grobid_xml":"https://content.openalex.org/works/W2602156049.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W54468324","https://openalex.org/W1923082386","https://openalex.org/W1967426040","https://openalex.org/W1979229593","https://openalex.org/W1988929438","https://openalex.org/W1989888272","https://openalex.org/W1994576782","https://openalex.org/W2051595037","https://openalex.org/W2060823770","https://openalex.org/W2077353422","https://openalex.org/W2087008771","https://openalex.org/W2103441770","https://openalex.org/W2111584304","https://openalex.org/W2119180969","https://openalex.org/W2131016694","https://openalex.org/W2133784891","https://openalex.org/W2142721632","https://openalex.org/W2147733682","https://openalex.org/W2150612144","https://openalex.org/W2153805608","https://openalex.org/W2157539385","https://openalex.org/W2183603658","https://openalex.org/W3098304617"],"related_works":["https://openalex.org/W2805859037","https://openalex.org/W2403609377","https://openalex.org/W2041048994","https://openalex.org/W4313342334","https://openalex.org/W4225751448","https://openalex.org/W3107980954","https://openalex.org/W2276490703","https://openalex.org/W3134891899","https://openalex.org/W4313584754","https://openalex.org/W4389900363"],"abstract_inverted_index":{"BACKGROUND:":[0],"NGS":[1],"technology":[2],"represents":[3],"a":[4,38,70,86,109,141,160,206,218,237],"powerful":[5],"alternative":[6],"to":[7,106,111,116,164,182,191,246],"the":[8,13,50,61,82,89,95,102,113,120,155,184,241,248,251],"standard":[9,83,173],"Sanger":[10],"sequencing":[11],"in":[12,37,49,55,119,159],"context":[14],"of":[15,65,73,85,101,123,140,203,209,244,250],"clinical":[16],"setting.":[17],"The":[18,99],"proprietary":[19],"software":[20],"that":[21,33,214,227],"are":[22,77],"generally":[23],"used":[24,48,118],"for":[25,41,57],"variant":[26,58,196,252],"calling":[27],"often":[28],"depend":[29],"on":[30,132],"preset":[31],"parameters":[32,56,90,115,187],"may":[34],"not":[35,78],"fit":[36],"satisfactory":[39],"manner":[40],"different":[42,151],"genes.":[43],"GATK,":[44],"which":[45,80],"is":[46,53,81],"widely":[47],"academic":[51],"world,":[52],"rich":[54],"calling.":[59,253],"However":[60],"self-adjusting":[62],"parameter":[63,231],"calibration":[64],"GATK":[66,228],"requires":[67],"data":[68],"from":[69,137],"large":[71],"number":[72],"exomes.":[74],"When":[75],"these":[76],"available,":[79],"condition":[84],"diagnostic":[87],"laboratory,":[88],"must":[91],"be":[92,117,234],"set":[93,107],"by":[94,128],"operator":[96],"(hard":[97],"filtering).":[98],"aim":[100],"present":[103,217],"paper":[104],"was":[105,126],"up":[108,181],"procedure":[110],"assess":[112],"best":[114],"hard":[121,229],"filtering":[122,230],"GATK.":[124],"This":[125],"pursued":[127],"using":[129],"classification":[130],"trees":[131,178],"true":[133,193],"and":[134,175,188,194],"false":[135,195,210],"variants":[136],"simulated":[138,147],"sequences":[139,169,202,216],"real":[142,161],"dataset":[143,162],"data.":[144],"RESULTS:":[145],"We":[146],"two":[148],"datasets,":[149],"with":[150,172],"coverages,":[152],"including":[153],"all":[154],"sequence":[156],"alterations":[157],"identified":[158],"according":[163],"their":[165],"observed":[166],"frequencies.":[167],"Simulated":[168],"were":[170,179],"aligned":[171],"protocols":[174],"then":[176],"regression":[177],"built":[180],"identify":[183],"most":[185],"reliable":[186],"cutoff":[189],"values":[190,232],"discriminate":[192],"calls.":[197],"Moreover,":[198],"we":[199],"analyzed":[200],"flanking":[201],"region":[204,243],"presenting":[205],"high":[207],"rate":[208],"positive":[211],"calls":[212],"observing":[213],"such":[215],"low":[219],"complexity":[220],"make":[221],"up.":[222],"CONCLUSIONS:":[223],"Our":[224],"results":[225],"showed":[226],"can":[233],"tailored":[235],"through":[236],"simulation":[238],"study":[239],"based-on":[240],"DNA":[242],"interest":[245],"ameliorate":[247],"accuracy":[249]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
