{"id":"https://openalex.org/W4311573638","doi":"https://doi.org/10.1093/bioinformatics/btac810","title":"Insane in the vembrane: filtering and transforming VCF/BCF files","display_name":"Insane in the vembrane: filtering and transforming VCF/BCF files","publication_year":2022,"publication_date":"2022-12-14","ids":{"openalex":"https://openalex.org/W4311573638","doi":"https://doi.org/10.1093/bioinformatics/btac810","pmid":"https://pubmed.ncbi.nlm.nih.gov/36519840"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac810","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac810/48520818/btac810.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":"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac810/48520818/btac810.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017856839","display_name":"Till Hartmann","orcid":"https://orcid.org/0000-0002-6993-347X"},"institutions":[{"id":"https://openalex.org/I62318514","display_name":"University of Duisburg-Essen","ror":"https://ror.org/04mz5ra38","country_code":"DE","type":"education","lineage":["https://openalex.org/I62318514"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Till Hartmann","raw_affiliation_strings":["Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany"],"raw_orcid":"https://orcid.org/0000-0002-6993-347X","affiliations":[{"raw_affiliation_string":"Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany","institution_ids":["https://openalex.org/I62318514"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102865092","display_name":"Christopher Schr\u00f6der","orcid":"https://orcid.org/0000-0002-4483-8951"},"institutions":[{"id":"https://openalex.org/I62318514","display_name":"University of Duisburg-Essen","ror":"https://ror.org/04mz5ra38","country_code":"DE","type":"education","lineage":["https://openalex.org/I62318514"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christopher Schr\u00f6der","raw_affiliation_strings":["Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany","institution_ids":["https://openalex.org/I62318514"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060203954","display_name":"Elias Kuthe","orcid":"https://orcid.org/0000-0002-4704-9536"},"institutions":[{"id":"https://openalex.org/I200332995","display_name":"TU Dortmund University","ror":"https://ror.org/01k97gp34","country_code":"DE","type":"education","lineage":["https://openalex.org/I200332995"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Elias Kuthe","raw_affiliation_strings":["Computer Science XI, TU Dortmund University , Dortmund 44227, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science XI, TU Dortmund University , Dortmund 44227, Germany","institution_ids":["https://openalex.org/I200332995"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108916122","display_name":"David L\u00e4hnemann","orcid":null},"institutions":[{"id":"https://openalex.org/I62318514","display_name":"University of Duisburg-Essen","ror":"https://ror.org/04mz5ra38","country_code":"DE","type":"education","lineage":["https://openalex.org/I62318514"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"David L\u00e4hnemann","raw_affiliation_strings":["Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany","Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9138-4112","affiliations":[{"raw_affiliation_string":"Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany","institution_ids":["https://openalex.org/I62318514"]},{"raw_affiliation_string":"Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany","institution_ids":["https://openalex.org/I62318514"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005124395","display_name":"Johannes K\u00f6ster","orcid":"https://orcid.org/0000-0001-9818-9320"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]},{"id":"https://openalex.org/I62318514","display_name":"University of Duisburg-Essen","ror":"https://ror.org/04mz5ra38","country_code":"DE","type":"education","lineage":["https://openalex.org/I62318514"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Johannes K\u00f6ster","raw_affiliation_strings":["Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany","Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Algorithms for Reproducible Bioinformatics, University Hospital Essen, University of Duisburg-Essen , Essen 45147, Germany","institution_ids":["https://openalex.org/I62318514"]},{"raw_affiliation_string":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02215, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210117453"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5017856839"],"corresponding_institution_ids":["https://openalex.org/I62318514"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1803,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.80323083,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.20149999856948853,"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":0.20149999856948853,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.11779999732971191,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.10490000247955322,"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":0.5457649827003479}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5457649827003479}],"mesh":[{"descriptor_ui":"D001523","descriptor_name":"Mental Disorders","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001523","descriptor_name":"Mental Disorders","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001523","descriptor_name":"Mental Disorders","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac810","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac810/48520818/btac810.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":"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:36519840","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36519840","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:9825764","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825764","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac810","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac810","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac810/48520818/btac810.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":"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/G3988035882","display_name":"SFB 876: Verf\u00fcgbarkeit von Information durch Analyse unter Ressourcenbeschr\u00e4nkung","funder_award_id":"124020371","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G617271991","display_name":null,"funder_award_id":"SFB876","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4311573638.pdf","grobid_xml":"https://content.openalex.org/works/W4311573638.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2029641872","https://openalex.org/W2106578986","https://openalex.org/W2149992227","https://openalex.org/W2417483443","https://openalex.org/W2768718979","https://openalex.org/W3180381598","https://openalex.org/W4282935730"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"present":[2],"vembrane":[3,56,72],"as":[4,52],"a":[5],"command":[6],"line":[7],"variant":[8],"call":[9,12],"format":[10,13],"(VCF)/binary":[11],"(BCF)":[14],"filtering":[15,22,31],"tool":[16],"that":[17],"consolidates":[18],"and":[19,41,50,93,103],"extends":[20],"the":[21,36,46,68],"functionality":[23],"of":[24,67,81],"previous":[25],"software":[26],"to":[27,76],"meet":[28],"any":[29],"imaginable":[30],"use":[32],"case.":[33],"Vembrane":[34],"exposes":[35],"VCF/BCF":[37],"file":[38],"type":[39],"specification":[40],"its":[42],"inofficial":[43],"extensions":[44],"by":[45,60,90],"annotation":[47],"tools":[48],"VEP":[49],"SnpEff":[51],"Python":[53,61,69],"data":[54,115],"structures.":[55],"filter":[57],"enables":[58],"filtration":[59],"expressions,":[62],"requiring":[63],"only":[64],"basic":[65],"knowledge":[66],"programming":[70],"language.":[71],"table":[73],"allows":[74],"users":[75],"generate":[77],"tables":[78],"from":[79],"subsets":[80],"annotations":[82],"or":[83],"functions":[84],"thereof.":[85],"Finally,":[86],"it":[87],"is":[88],"fast,":[89],"using":[91],"pysam":[92],"relying":[94],"on":[95],"lazy":[96],"evaluation.":[97],"AVAILABILITY":[98],"AND":[99],"IMPLEMENTATION:":[100],"Source":[101],"code":[102],"installation":[104],"instructions":[105],"are":[106,116],"available":[107,117],"at":[108,118],"github.com/vembrane/vembrane":[109],"(doi:":[110],"10.5281/zenodo.7003981).":[111],"SUPPLEMENTARY":[112],"INFORMATION:":[113],"Supplementary":[114],"Bioinformatics":[119],"online.":[120]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2025-10-10T00:00:00"}
