{"id":"https://openalex.org/W2795892343","doi":"https://doi.org/10.1093/bioinformatics/bty192","title":"Efficient population-scale variant analysis and prioritization with VAPr","display_name":"Efficient population-scale variant analysis and prioritization with VAPr","publication_year":2018,"publication_date":"2018-04-05","ids":{"openalex":"https://openalex.org/W2795892343","doi":"https://doi.org/10.1093/bioinformatics/bty192","mag":"2795892343","pmid":"https://pubmed.ncbi.nlm.nih.gov/29659724"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2843/25441974/bty192.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/34/16/2843/25441974/bty192.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061546513","display_name":"Amanda Birmingham","orcid":"https://orcid.org/0000-0002-4117-3317"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amanda Birmingham","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110326934","display_name":"Adam M. Mark","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam M Mark","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039633969","display_name":"Carlo Mazzaferro","orcid":"https://orcid.org/0000-0002-7869-3500"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carlo Mazzaferro","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102546014","display_name":"Guorong Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guorong Xu","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058181019","display_name":"Kathleen M. Fisch","orcid":"https://orcid.org/0000-0002-0117-7444"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kathleen M Fisch","raw_affiliation_strings":["Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-0117-7444","affiliations":[{"raw_affiliation_string":"Center for Computational Biology and Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5058181019"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1726,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.59964482,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"34","issue":"16","first_page":"2843","last_page":"2845"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.8428999781608582,"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":0.8428999781608582,"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":0.06840000301599503,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.06390000134706497,"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/python","display_name":"Python (programming language)","score":0.8450629711151123},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.7904698252677917},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7843550443649292},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6955602169036865},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6327831149101257},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.572433590888977},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4998948574066162},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.49693062901496887},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.46455878019332886},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.448991984128952},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2749215364456177},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.1872439682483673},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10999700427055359}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8450629711151123},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7904698252677917},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7843550443649292},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6955602169036865},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6327831149101257},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.572433590888977},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4998948574066162},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.49693062901496887},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.46455878019332886},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.448991984128952},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2749215364456177},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.1872439682483673},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10999700427055359},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"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/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","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},{"descriptor_ui":"D059472","descriptor_name":"Exome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2843/25441974/bty192.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:29659724","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29659724","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:europepmc.org:5640756","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6084604","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty192","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty192","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2843/25441974/bty192.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":[],"awards":[{"id":"https://openalex.org/G3144457050","display_name":null,"funder_award_id":"UL1 TR001442","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G7347388112","display_name":null,"funder_award_id":"P50 GM085764","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7683705120","display_name":null,"funder_award_id":"UL1TR001442","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320316438","display_name":"Georgia Clinical and Translational Science Alliance","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1977646793","https://openalex.org/W1984068087","https://openalex.org/W2004045226","https://openalex.org/W2051075975","https://openalex.org/W2149992227","https://openalex.org/W2168440186","https://openalex.org/W2204224788","https://openalex.org/W2256016639","https://openalex.org/W2347037915","https://openalex.org/W2548107498"],"related_works":["https://openalex.org/W4220666916","https://openalex.org/W3136652852","https://openalex.org/W4221030787","https://openalex.org/W2796515132","https://openalex.org/W3042189086","https://openalex.org/W2331230230","https://openalex.org/W2795892343","https://openalex.org/W3092585739","https://openalex.org/W2808731431","https://openalex.org/W2317724253"],"abstract_inverted_index":{"Summary:":[0],"With":[1],"the":[2,29,88],"growing":[3],"availability":[4],"of":[5,64],"population-scale":[6],"whole-exome":[7],"and":[8,34,43,49,55,59,62,72,79,85,103],"whole-genome":[9],"sequencing,":[10],"demand":[11],"for":[12,82],"reproducible,":[13],"scalable":[14,60],"variant":[15],"analysis":[16,61],"has":[17],"spread":[18],"within":[19],"genomic":[20,65],"research":[21],"communities.":[22],"To":[23],"address":[24],"this":[25],"need,":[26],"we":[27],"introduce":[28],"Python":[30,78],"package":[31,93],"Variant":[32],"Analysis":[33],"Prioritization":[35],"(VAPr).":[36],"VAPr":[37,74],"leverages":[38],"existing":[39],"annotation":[40],"tools":[41],"ANNOVAR":[42],"MyVariant.info":[44],"with":[45],"MongoDB-based":[46],"flexible":[47],"storage":[48],"filtering":[50],"functionality.":[51],"It":[52],"offers":[53],"biologists":[54],"bioinformatics":[56],"generalists":[57],"easy-to-use":[58],"prioritization":[63],"variants":[66],"from":[67],"large":[68],"cohort":[69],"studies.":[70],"Availability":[71],"implementation:":[73],"is":[75,80,94],"developed":[76],"in":[77],"available":[81,95],"free":[83],"use":[84],"extension":[86],"under":[87],"MIT":[89],"License.":[90],"An":[91],"install":[92],"on":[96,107],"PyPi":[97],"at":[98,109],"https://pypi.python.org/pypi/VAPr,":[99],"while":[100],"source":[101],"code":[102],"extensive":[104],"documentation":[105],"are":[106],"GitHub":[108],"https://github.com/ucsd-ccbb/VAPr.":[110]},"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}