{"id":"https://openalex.org/W4391262162","doi":"https://doi.org/10.1093/bioinformatics/btae049","title":"vcfpp: a C++ API for rapid processing of the variant call format","display_name":"vcfpp: a C++ API for rapid processing of the variant call format","publication_year":2024,"publication_date":"2024-01-23","ids":{"openalex":"https://openalex.org/W4391262162","doi":"https://doi.org/10.1093/bioinformatics/btae049","pmid":"https://pubmed.ncbi.nlm.nih.gov/38273677"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae049","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae049/56423149/btae049.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae049/56423149/btae049.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100699757","display_name":"Zilong Li","orcid":"https://orcid.org/0000-0001-5859-2078"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I4210088332","display_name":"University College Copenhagen","ror":"https://ror.org/004r9h172","country_code":"DK","type":"education","lineage":["https://openalex.org/I4210088332"]},{"id":"https://openalex.org/I83467386","display_name":"IT University of Copenhagen","ror":"https://ror.org/02309jg23","country_code":"DK","type":"education","lineage":["https://openalex.org/I83467386"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Zilong Li","raw_affiliation_strings":["Section for Computational and RNA Biology, University of Copenhagen , Copenhagen 2200, Denmark","Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, 2200, Denmark"],"raw_orcid":"https://orcid.org/0000-0001-5859-2078","affiliations":[{"raw_affiliation_string":"Section for Computational and RNA Biology, University of Copenhagen , Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I83467386","https://openalex.org/I124055696","https://openalex.org/I4210088332"]},{"raw_affiliation_string":"Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, 2200, Denmark","institution_ids":["https://openalex.org/I124055696"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100699757"],"corresponding_institution_ids":["https://openalex.org/I124055696","https://openalex.org/I4210088332","https://openalex.org/I83467386"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.5734,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.84562884,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"40","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10639","display_name":"Advanced Software Engineering Methodologies","score":0.2782999873161316,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10639","display_name":"Advanced Software Engineering Methodologies","score":0.2782999873161316,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10260","display_name":"Software Engineering Research","score":0.22429999709129333,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12127","display_name":"Software System Performance and Reliability","score":0.1315000057220459,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6824980974197388},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3704230785369873}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6824980974197388},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3704230785369873}],"mesh":[{"descriptor_ui":"D000077558","descriptor_name":"Big Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077558","descriptor_name":"Big Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077558","descriptor_name":"Big Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077558","descriptor_name":"Big Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077558","descriptor_name":"Big Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077558","descriptor_name":"Big Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btae049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae049","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae049/56423149/btae049.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38273677","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38273677","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},{"id":"pmh:oai:pubmedcentral.nih.gov:10868310","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10868310","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10868310/pdf/btae049.pdf","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/23cc8a92-8c8c-479f-afc7-eee668ef9860","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/23cc8a92-8c8c-479f-afc7-eee668ef9860","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"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":"Li , Z 2024 , ' vcfpp : a C++ API for rapid processing of the variant call format ' , Bioinformatics , vol. 40 , no. 2 , btae049 . https://doi.org/10.1093/bioinformatics/btae049","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae049","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae049/56423149/btae049.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3798523387","display_name":null,"funder_award_id":"NNF20OC0061343","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G8178235528","display_name":null,"funder_award_id":"NNF20OC0061343","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"}],"funders":[{"id":"https://openalex.org/F4320320290","display_name":"University of Oxford","ror":"https://ror.org/052gg0110"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391262162.pdf"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2108234281","https://openalex.org/W2149992227","https://openalex.org/W2159325249","https://openalex.org/W2473818600","https://openalex.org/W2474836229","https://openalex.org/W2586169357","https://openalex.org/W2951541096","https://openalex.org/W3131443014","https://openalex.org/W4206754124","https://openalex.org/W4282935730","https://openalex.org/W4294012180","https://openalex.org/W4310167947","https://openalex.org/W4411392672"],"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":{"MOTIVATION:":[0],"Given":[1],"the":[2,6,71,76],"widespread":[3],"use":[4],"of":[5,45,78],"variant":[7],"call":[8],"format":[9],"(VCF/BCF)":[10],"coupled":[11],"with":[12,83],"continuous":[13],"surge":[14],"in":[15,47,62],"big":[16],"data,":[17],"there":[18],"remains":[19],"a":[20,42,48,79],"perpetual":[21],"demand":[22],"for":[23,86],"fast":[24],"and":[25,60,88],"flexible":[26],"methods":[27],"to":[28,55,64,74],"manipulate":[29,56],"these":[30],"comprehensive":[31],"formats":[32],"across":[33],"various":[34],"programming":[35],"languages.":[36],"RESULTS:":[37],"This":[38],"work":[39,69],"presents":[40],"vcfpp,":[41,84],"C++":[43],"API":[44],"HTSlib":[46],"single":[49],"file,":[50],"providing":[51],"an":[52],"intuitive":[53],"interface":[54],"VCF/BCF":[57],"files":[58],"rapidly":[59],"safely,":[61],"addition":[63],"being":[65],"portable.":[66],"Moreover,":[67],"this":[68],"introduces":[70],"vcfppR":[72,103],"package":[73,82],"demonstrate":[75],"development":[77],"high-performance":[80],"R":[81],"allowing":[85],"rapid":[87],"straightforward":[89],"variants":[90],"analyses.":[91],"AVAILABILITY":[92],"AND":[93],"IMPLEMENTATION:":[94],"vcfpp":[95],"is":[96,104],"available":[97,105],"from":[98,106],"https://github.com/Zilong-Li/vcfpp":[99],"under":[100],"MIT":[101],"license.":[102],"https://cran.r-project.org/web/packages/vcfppR.":[107]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
