{"id":"https://openalex.org/W2491236485","doi":"https://doi.org/10.1093/bib/bbw069","title":"Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations","display_name":"Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations","publication_year":2016,"publication_date":"2016-07-29","ids":{"openalex":"https://openalex.org/W2491236485","doi":"https://doi.org/10.1093/bib/bbw069","mag":"2491236485","pmid":"https://pubmed.ncbi.nlm.nih.gov/27473065"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbw069","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbw069","pdf_url":"https://academic.oup.com/bib/article-pdf/18/6/973/25603446/bbw069.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/bib/article-pdf/18/6/973/25603446/bbw069.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067865294","display_name":"Zhifu Sun","orcid":"https://orcid.org/0000-0001-8461-7523"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhifu Sun","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053182366","display_name":"Aditya Bhagwate","orcid":"https://orcid.org/0000-0003-0192-9594"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aditya Bhagwate","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068134362","display_name":"Naresh Prodduturi","orcid":null},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Naresh Prodduturi","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048841778","display_name":"Ping Yang","orcid":"https://orcid.org/0000-0002-6977-8449"},"institutions":[{"id":"https://openalex.org/I4210146710","display_name":"Mayo Clinic in Florida","ror":"https://ror.org/03zzw1w08","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723","https://openalex.org/I4210146710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ping Yang","raw_affiliation_strings":["Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I4210146710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071782757","display_name":"Jean\u2010Pierre Kocher","orcid":"https://orcid.org/0000-0002-0260-6773"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jean-Pierre A. Kocher","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067865294"],"corresponding_institution_ids":["https://openalex.org/I1330342723"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":4.0086,"has_fulltext":false,"cited_by_count":52,"citation_normalized_percentile":{"value":0.94222178,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"18","issue":"6","first_page":"bbw069","last_page":"bbw069"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9983000159263611,"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/T11482","display_name":"RNA modifications and cancer","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":0.9755284786224365},{"id":"https://openalex.org/keywords/indel-mutation","display_name":"INDEL Mutation","score":0.7726122736930847},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6275603175163269},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5354196429252625},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5008821487426758},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.48808014392852783},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4824688732624054},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.4782937169075012},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4671233296394348},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4199655055999756},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4138643741607666},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.38539159297943115},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.36455395817756653},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17832383513450623},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.10324740409851074}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.9755284786224365},{"id":"https://openalex.org/C2910714999","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"INDEL Mutation","level":5,"score":0.7726122736930847},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6275603175163269},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5354196429252625},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5008821487426758},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48808014392852783},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4824688732624054},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.4782937169075012},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4671233296394348},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4199655055999756},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4138643741607666},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.38539159297943115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.36455395817756653},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17832383513450623},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.10324740409851074},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","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":"D000465","descriptor_name":"Algorithms","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016022","descriptor_name":"Case-Control Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016022","descriptor_name":"Case-Control Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016022","descriptor_name":"Case-Control Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbw069","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbw069","pdf_url":"https://academic.oup.com/bib/article-pdf/18/6/973/25603446/bbw069.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27473065","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27473065","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:5072890","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5862335","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/bib/bbw069","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbw069","pdf_url":"https://academic.oup.com/bib/article-pdf/18/6/973/25603446/bbw069.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.7599999904632568}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1514134885","https://openalex.org/W1572402121","https://openalex.org/W1596062789","https://openalex.org/W1882576502","https://openalex.org/W1911918948","https://openalex.org/W1963590871","https://openalex.org/W1964477845","https://openalex.org/W1973489592","https://openalex.org/W1977269166","https://openalex.org/W1985604190","https://openalex.org/W1993023683","https://openalex.org/W2000875411","https://openalex.org/W2054576015","https://openalex.org/W2071480068","https://openalex.org/W2096173343","https://openalex.org/W2096441981","https://openalex.org/W2097065948","https://openalex.org/W2099377894","https://openalex.org/W2102278945","https://openalex.org/W2102772400","https://openalex.org/W2103441770","https://openalex.org/W2106314269","https://openalex.org/W2119180969","https://openalex.org/W2124465358","https://openalex.org/W2124985265","https://openalex.org/W2136145671","https://openalex.org/W2138601221","https://openalex.org/W2140729960","https://openalex.org/W2141458291","https://openalex.org/W2142518990","https://openalex.org/W2146290346","https://openalex.org/W2151016309","https://openalex.org/W2151794156","https://openalex.org/W2155943701","https://openalex.org/W2158336776","https://openalex.org/W2161815151","https://openalex.org/W2162116127","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2182731941","https://openalex.org/W2190569576","https://openalex.org/W2271404980","https://openalex.org/W4247053599"],"related_works":["https://openalex.org/W2135846417","https://openalex.org/W2140698435","https://openalex.org/W2900160090","https://openalex.org/W2810280786","https://openalex.org/W2083543262","https://openalex.org/W2396424000","https://openalex.org/W3158393486","https://openalex.org/W3021382431","https://openalex.org/W2046092378","https://openalex.org/W1984359833"],"abstract_inverted_index":{"Driver":[0],"somatic":[1,102],"mutations":[2,53],"are":[3,19,83,213],"a":[4,7,106,146],"hallmark":[5],"of":[6,28,108,149,227],"tumor":[8,23],"that":[9,129,242],"can":[10,61,231,243],"be":[11,62,232,244],"used":[12,94,214,234,245],"for":[13,122,138,194,206,235,246],"diagnosis":[14],"and":[15,54,74,82,101,113,141,185,215,238],"targeted":[16],"therapy.":[17],"Mutations":[18],"primarily":[20],"detected":[21],"from":[22,65,157],"DNA.":[24],"As":[25],"dynamic":[26],"molecules":[27],"gene":[29,45],"activities,":[30],"transcriptome":[31],"profiling":[32],"by":[33,85,168],"RNA":[34],"sequence":[35,77,153,169],"(RNA-seq)":[36],"is":[37,118,133,166],"becoming":[38],"increasingly":[39],"popular,":[40],"which":[41],"not":[42,158],"only":[43],"measures":[44],"expression":[46],"but":[47],"also":[48],"structural":[49],"variations":[50],"such":[51],"as":[52],"fusion":[55],"transcripts.":[56],"Although":[57],"single-nucleotide":[58],"variants":[59],"(SNVs)":[60],"easily":[63],"identified":[64],"RNA-seq,":[66],"intermediate":[67],"long":[68],"insertions/deletions":[69],"(indels":[70],">":[71],"2":[72],"bases":[73],"less":[75],"than":[76],"reads)":[78],"cause":[79],"significant":[80],"challenges":[81],"ignored":[84],"most":[86,135],"RNA-seq":[87,95,131,211,230],"analysis":[88,96],"tools.":[89],"This":[90],"study":[91],"evaluates":[92],"commonly":[93],"programs":[97,144,175,187],"along":[98],"with":[99,111,155,188,220],"variant":[100,173],"mutation":[103,240],"callers":[104],"in":[105,182],"series":[107],"data":[109],"sets":[110],"simulated":[112],"known":[114],"indels.":[115],"The":[116,164],"aim":[117],"to":[119,151,161],"develop":[120],"strategies":[121],"accurate":[123],"indel":[124,139,195,207,239],"detection.":[125],"Our":[126],"results":[127],"show":[128],"the":[130,134,142,183,186,199,217],"alignment":[132,184],"important":[136],"step":[137],"identification":[140],"evaluated":[143],"have":[145,202],"wide":[147],"range":[148],"sensitivity":[150,165],"map":[152],"reads":[154,193],"indels,":[156],"at":[159],"all":[160],"decently":[162],"sensitive.":[163],"impacted":[167],"read":[170],"lengths.":[171],"Most":[172],"calling":[174],"rely":[176],"on":[177,198],"hard":[178],"evidence":[179],"indels":[180],"marked":[181],"realignment":[189],"may":[190],"use":[191],"soft-clipped":[192],"inferencing.":[196],"Based":[197],"observations,":[200],"we":[201],"provided":[203],"practical":[204],"recommendations":[205],"detection":[208,241],"when":[209],"different":[210],"aligners":[212],"demonstrated":[216],"best":[218],"option":[219],"highly":[221],"reliable":[222],"results.":[223],"With":[224],"careful":[225],"customization":[226],"bioinformatics":[228],"algorithms,":[229],"reliably":[233],"both":[236],"SNV":[237],"clinical":[247],"decision-making.":[248]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":5}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}