{"id":"https://openalex.org/W3131770457","doi":"https://doi.org/10.1186/s12859-021-03995-y","title":"FiNGS: high quality somatic mutations using filters for next generation sequencing","display_name":"FiNGS: high quality somatic mutations using filters for next generation sequencing","publication_year":2021,"publication_date":"2021-02-18","ids":{"openalex":"https://openalex.org/W3131770457","doi":"https://doi.org/10.1186/s12859-021-03995-y","mag":"3131770457","pmid":"https://pubmed.ncbi.nlm.nih.gov/33602113"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-03995-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03995-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03995-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03995-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084133067","display_name":"Christopher P. Wardell","orcid":"https://orcid.org/0000-0002-9416-7818"},"institutions":[{"id":"https://openalex.org/I79620101","display_name":"University of Arkansas for Medical Sciences","ror":"https://ror.org/00xcryt71","country_code":"US","type":"education","lineage":["https://openalex.org/I79620101"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Christopher Paul Wardell","raw_affiliation_strings":["Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA. cpwardell@uams.edu","Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA"],"raw_orcid":"https://orcid.org/0000-0002-9416-7818","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA. cpwardell@uams.edu","institution_ids":["https://openalex.org/I79620101"]},{"raw_affiliation_string":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA","institution_ids":["https://openalex.org/I79620101"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090728387","display_name":"Cody Ashby","orcid":"https://orcid.org/0000-0002-9361-0283"},"institutions":[{"id":"https://openalex.org/I79620101","display_name":"University of Arkansas for Medical Sciences","ror":"https://ror.org/00xcryt71","country_code":"US","type":"education","lineage":["https://openalex.org/I79620101"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cody Ashby","raw_affiliation_strings":["Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA","institution_ids":["https://openalex.org/I79620101"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007618693","display_name":"Michael Bauer","orcid":"https://orcid.org/0000-0003-2498-7295"},"institutions":[{"id":"https://openalex.org/I79620101","display_name":"University of Arkansas for Medical Sciences","ror":"https://ror.org/00xcryt71","country_code":"US","type":"education","lineage":["https://openalex.org/I79620101"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Anton Bauer","raw_affiliation_strings":["Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA","institution_ids":["https://openalex.org/I79620101"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5084133067"],"corresponding_institution_ids":["https://openalex.org/I79620101"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.9453,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.68924874,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"77","last_page":"77"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9689000248908997,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9689000248908997,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.014499999582767487,"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":0.004999999888241291,"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":0.713138222694397},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.6732839345932007},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.5289027094841003},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5041319131851196},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4579561650753021},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4249858856201172},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.352372407913208},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.24004611372947693},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18513250350952148},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1836007833480835},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10011473298072815}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.713138222694397},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.6732839345932007},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.5289027094841003},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5041319131851196},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4579561650753021},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4249858856201172},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.352372407913208},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24004611372947693},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18513250350952148},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1836007833480835},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10011473298072815},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","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":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-021-03995-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03995-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03995-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33602113","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33602113","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:54d6ebbc829b4647a51fb4529e0b44ca","is_oa":true,"landing_page_url":"https://doaj.org/article/54d6ebbc829b4647a51fb4529e0b44ca","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-6 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7890800","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7890800","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-03995-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03995-y","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03995-y","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3131770457.pdf","grobid_xml":"https://content.openalex.org/works/W3131770457.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2103441770","https://openalex.org/W2119180969","https://openalex.org/W2138601221","https://openalex.org/W2149992227","https://openalex.org/W2155943701","https://openalex.org/W2192272998","https://openalex.org/W2613409207","https://openalex.org/W2760673044","https://openalex.org/W2761175901","https://openalex.org/W2765745983","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1557094818","https://openalex.org/W2183246718","https://openalex.org/W2099261052","https://openalex.org/W3209204065","https://openalex.org/W2105707930","https://openalex.org/W1755711892","https://openalex.org/W2160907113","https://openalex.org/W2164205946","https://openalex.org/W2070813941","https://openalex.org/W2348583279"],"abstract_inverted_index":{"BACKGROUND:":[0],"Somatic":[1],"variant":[2,45,103,153],"callers":[3],"are":[4,16,142],"used":[5],"to":[6,77,124,132,168],"find":[7],"mutations":[8],"in":[9,57],"sequencing":[10,89,163],"data":[11,29,90],"from":[12],"cancer":[13],"samples.":[14],"They":[15],"very":[17],"sensitive":[18],"and":[19,47,84,106,135,139,150,158,170,176],"have":[20,66],"high":[21],"recall,":[22],"but":[23],"also":[24],"may":[25],"produce":[26],"low":[27],"precision":[28,100],"with":[30,121,137,181],"a":[31,58,122],"large":[32],"proportion":[33],"of":[34,54,101,179],"false":[35],"positives.":[36],"Further":[37],"ad":[38],"hoc":[39],"filtering":[40,53,80,174],"is":[41,130],"commonly":[42],"performed":[43],"after":[44],"calling":[46],"before":[48],"further":[49],"analysis.":[50],"Improving":[51],"the":[52,99,114,146],"somatic":[55,127],"variants":[56,128],"reproducible":[59],"way":[60],"represents":[61],"an":[62],"unmet":[63],"need.":[64],"We":[65],"developed":[67],"Filters":[68],"for":[69,113],"Next":[70],"Generation":[71],"Sequencing":[72],"(FiNGS),":[73],"software":[74],"written":[75],"specifically":[76],"address":[78],"these":[79,180],"issues.":[81],"RESULTS:":[82],"Developed":[83],"tested":[85],"using":[86],"publicly":[87],"available":[88],"sets,":[91],"we":[92],"demonstrate":[93],"that":[94,129,141],"FiNGS":[95,118],"reliably":[96],"improves":[97],"upon":[98],"default":[102],"caller":[104],"outputs":[105],"performs":[107],"better":[108],"than":[109],"other":[110],"tools":[111],"designed":[112],"same":[115],"task.":[116],"CONCLUSIONS:":[117],"provides":[119],"researchers":[120],"tool":[123],"reproducibly":[125],"filter":[126],"simple":[131,177],"both":[133],"deploy":[134],"use,":[136],"filters":[138],"thresholds":[140],"fully":[143],"configurable":[144],"by":[145],"user.":[147],"It":[148,165],"ingests":[149],"emits":[151],"standard":[152],"call":[154],"format":[155],"(VCF)":[156],"files":[157],"will":[159],"slot":[160],"into":[161],"existing":[162],"pipelines.":[164],"allows":[166],"users":[167],"develop":[169],"implement":[171],"their":[172],"own":[173],"strategies":[175],"sharing":[178],"others.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
