{"id":"https://openalex.org/W2949787845","doi":"https://doi.org/10.1093/bioinformatics/btx100","title":"BCFtools/csq: haplotype-aware variant consequences","display_name":"BCFtools/csq: haplotype-aware variant consequences","publication_year":2017,"publication_date":"2017-02-15","ids":{"openalex":"https://openalex.org/W2949787845","doi":"https://doi.org/10.1093/bioinformatics/btx100","mag":"2949787845","pmid":"https://pubmed.ncbi.nlm.nih.gov/28205675"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx100","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx100","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2037/25155875/btx100.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/33/13/2037/25155875/btx100.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038201103","display_name":"Petr Danecek","orcid":"https://orcid.org/0000-0002-4159-1666"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Petr Danecek","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK","Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030669774","display_name":"Shane McCarthy","orcid":"https://orcid.org/0000-0002-2715-4187"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shane A McCarthy","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK","Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5038201103"],"corresponding_institution_ids":["https://openalex.org/I2802476451"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":9.318,"has_fulltext":true,"cited_by_count":486,"citation_normalized_percentile":{"value":0.98641781,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"33","issue":"13","first_page":"2037","last_page":"2039"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9980000257492065,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9944999814033508,"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/indel","display_name":"Indel","score":0.8802998065948486},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.7705916166305542},{"id":"https://openalex.org/keywords/indel-mutation","display_name":"INDEL Mutation","score":0.6499338746070862},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6413813233375549},{"id":"https://openalex.org/keywords/1000-genomes-project","display_name":"1000 Genomes Project","score":0.5873873233795166},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5143357515335083},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.4925718903541565},{"id":"https://openalex.org/keywords/categorization","display_name":"Categorization","score":0.47524523735046387},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46777310967445374},{"id":"https://openalex.org/keywords/sanger-sequencing","display_name":"Sanger sequencing","score":0.45465943217277527},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4523218870162964},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31856733560562134},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2855316996574402},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2229110598564148},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.20646673440933228},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.19240757822990417},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15839883685112}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.8802998065948486},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.7705916166305542},{"id":"https://openalex.org/C2910714999","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"INDEL Mutation","level":5,"score":0.6499338746070862},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6413813233375549},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.5873873233795166},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5143357515335083},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.4925718903541565},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.47524523735046387},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46777310967445374},{"id":"https://openalex.org/C76818968","wikidata":"https://www.wikidata.org/wiki/Q181940","display_name":"Sanger sequencing","level":4,"score":0.45465943217277527},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4523218870162964},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31856733560562134},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2855316996574402},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2229110598564148},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.20646673440933228},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.19240757822990417},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15839883685112},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","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":"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":"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},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":"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":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx100","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx100","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2037/25155875/btx100.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:28205675","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28205675","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:5870570","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5870570","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/btx100","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx100","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/13/2037/25155875/btx100.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":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.49000000953674316},{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G1886719193","display_name":null,"funder_award_id":"WT098051","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"},{"id":"https://openalex.org/G4839860845","display_name":null,"funder_award_id":"098051","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G7291792222","display_name":null,"funder_award_id":"WT098051","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G8666890344","display_name":null,"funder_award_id":"098051","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320307874","display_name":"Wellcome","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949787845.pdf","grobid_xml":"https://content.openalex.org/works/W2949787845.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1852222710","https://openalex.org/W1984068087","https://openalex.org/W2106578986","https://openalex.org/W2145809383","https://openalex.org/W2256016639","https://openalex.org/W2264578395","https://openalex.org/W2309446455","https://openalex.org/W2417483443","https://openalex.org/W2511515754","https://openalex.org/W2529241974","https://openalex.org/W2949138186"],"related_works":["https://openalex.org/W4385750939","https://openalex.org/W1882576502","https://openalex.org/W2529614973","https://openalex.org/W2167094946","https://openalex.org/W2160515792","https://openalex.org/W3103976079","https://openalex.org/W1508404210","https://openalex.org/W2744064477","https://openalex.org/W2156272823","https://openalex.org/W4389228387"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":22},{"year":2025,"cited_by_count":70},{"year":2024,"cited_by_count":76},{"year":2023,"cited_by_count":72},{"year":2022,"cited_by_count":80},{"year":2021,"cited_by_count":83},{"year":2020,"cited_by_count":54},{"year":2019,"cited_by_count":20},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}