{"id":"https://openalex.org/W2727237484","doi":"https://doi.org/10.1093/bioinformatics/btx422","title":"VCF-Explorer: filtering and analysing whole genome VCF files","display_name":"VCF-Explorer: filtering and analysing whole genome VCF files","publication_year":2017,"publication_date":"2017-07-06","ids":{"openalex":"https://openalex.org/W2727237484","doi":"https://doi.org/10.1093/bioinformatics/btx422","mag":"2727237484","pmid":"https://pubmed.ncbi.nlm.nih.gov/29036499"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx422","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx422","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/21/3468/25166051/btx422.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/21/3468/25166051/btx422.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037293831","display_name":"Mete Akg\u00fcn","orcid":"https://orcid.org/0000-0003-4088-2784"},"institutions":[{"id":"https://openalex.org/I198068145","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77","country_code":"TR","type":"government","lineage":["https://openalex.org/I198068145"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Mete Akg\u00fcn","raw_affiliation_strings":["The Scientific and Technological Research Council of Turkey (T\u00dcB\u0130TAK), Gebze, Kocaeli, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Scientific and Technological Research Council of Turkey (T\u00dcB\u0130TAK), Gebze, Kocaeli, Turkey","institution_ids":["https://openalex.org/I198068145"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063730885","display_name":"H\u00fcseyin Demirci","orcid":"https://orcid.org/0000-0002-0538-2074"},"institutions":[{"id":"https://openalex.org/I198068145","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77","country_code":"TR","type":"government","lineage":["https://openalex.org/I198068145"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"H\u00fcseyin Demirci","raw_affiliation_strings":["The Scientific and Technological Research Council of Turkey (T\u00dcB\u0130TAK), Gebze, Kocaeli, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Scientific and Technological Research Council of Turkey (T\u00dcB\u0130TAK), Gebze, Kocaeli, Turkey","institution_ids":["https://openalex.org/I198068145"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037293831"],"corresponding_institution_ids":["https://openalex.org/I198068145"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5606,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.66315697,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"33","issue":"21","first_page":"3468","last_page":"3470"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6812999844551086,"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":0.6812999844551086,"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":0.17479999363422394,"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":0.05380000174045563,"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":0.788277268409729},{"id":"https://openalex.org/keywords/laptop","display_name":"Laptop","score":0.6672927141189575},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4999549388885498},{"id":"https://openalex.org/keywords/exome","display_name":"Exome","score":0.480225145816803},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.4218078851699829},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2696802616119385},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12042281031608582},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.11226281523704529},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07906767725944519}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.788277268409729},{"id":"https://openalex.org/C2780008327","wikidata":"https://www.wikidata.org/wiki/Q3962","display_name":"Laptop","level":2,"score":0.6672927141189575},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4999549388885498},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.480225145816803},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.4218078851699829},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2696802616119385},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12042281031608582},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.11226281523704529},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07906767725944519},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000191","qualifier_name":"economics","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx422","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx422","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/21/3468/25166051/btx422.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29036499","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29036499","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx422","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx422","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/21/3468/25166051/btx422.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5400000214576721,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W1986050428","https://openalex.org/W2104549677","https://openalex.org/W2113534011","https://openalex.org/W2149870803","https://openalex.org/W2171203723","https://openalex.org/W2281926395","https://openalex.org/W2467057731"],"related_works":["https://openalex.org/W2093932542","https://openalex.org/W2043256480","https://openalex.org/W2400191746","https://openalex.org/W1983406990","https://openalex.org/W2094815267","https://openalex.org/W2484239316","https://openalex.org/W3024198590","https://openalex.org/W4367844067","https://openalex.org/W2104595023","https://openalex.org/W2106924416"],"abstract_inverted_index":{"SUMMARY:":[0],"The":[1,20],"decreasing":[2],"cost":[3],"in":[4,32,124],"high-throughput":[5],"technologies":[6],"led":[7],"to":[8,25,46,86,91,101,135],"a":[9,29,68,132,136],"number":[10],"of":[11,15,17,35,39,73,110],"sequencing":[12],"projects":[13],"consisting":[14],"thousands":[16],"whole":[18,26,59],"genomes.":[19],"paradigm":[21],"shift":[22],"from":[23,131],"exome":[24,48],"genome":[27,60],"brings":[28],"significant":[30],"increase":[31],"the":[33,40,89],"size":[34],"output":[36],"files.":[37,76],"Most":[38],"existing":[41],"tools":[42],"which":[43],"are":[44,50,155],"developed":[45],"analyse":[47],"files":[49,56],"not":[51],"adequate":[52],"for":[53],"larger":[54],"VCF":[55],"produced":[57],"by":[58],"studies.":[61],"In":[62],"this":[63],"work":[64],"we":[65],"present":[66],"VCF-Explorer,":[67],"variant":[69,114],"analysis":[70,90],"software":[71],"capable":[72],"handling":[74],"large":[75],"Memory":[77],"efficiency":[78],"and":[79,115,127],"avoiding":[80],"computationally":[81],"costly":[82],"pre-processing":[83],"step":[84],"enable":[85],"carry":[87],"out":[88],"be":[92,122],"performed":[93],"with":[94],"ordinary":[95],"computers.":[96],"VCF-Explorer":[97,120,143],"provides":[98],"an":[99],"easy":[100],"use":[102],"environment":[103],"where":[104],"users":[105],"can":[106,121],"define":[107],"various":[108],"types":[109],"queries":[111],"based":[112],"on":[113],"sample":[116],"genotype":[117],"level":[118],"annotations.":[119],"run":[123],"different":[125],"environments":[126],"computational":[128],"platforms":[129],"ranging":[130],"standard":[133],"laptop":[134],"high":[137],"performance":[138],"server.":[139],"AVAILABILITY":[140],"AND":[141],"IMPLEMENTATION:":[142],"is":[144],"freely":[145],"available":[146,156],"at:":[147],"http://vcfexplorer.sourceforge.net/.":[148],"CONTACT:":[149],"mete.akgun@tubitak.gov.tr.":[150],"SUPPLEMENTARY":[151],"INFORMATION:":[152],"Supplementary":[153],"data":[154],"at":[157],"Bioinformatics":[158],"online.":[159]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
