{"id":"https://openalex.org/W2988700766","doi":"https://doi.org/10.1186/s12859-019-3169-7","title":"Recommendations for performance optimizations when using GATK3.8 and GATK4","display_name":"Recommendations for performance optimizations when using GATK3.8 and GATK4","publication_year":2019,"publication_date":"2019-11-08","ids":{"openalex":"https://openalex.org/W2988700766","doi":"https://doi.org/10.1186/s12859-019-3169-7","mag":"2988700766","pmid":"https://pubmed.ncbi.nlm.nih.gov/31703611"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3169-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3169-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3169-7","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/s12859-019-3169-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070069424","display_name":"Jacob R. Heldenbrand","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I4210135837","display_name":"National Center for Supercomputing Applications","ror":"https://ror.org/03r10zj06","country_code":"US","type":"facility","lineage":["https://openalex.org/I157725225","https://openalex.org/I4210135837"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob R Heldenbrand","raw_affiliation_strings":["National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W. Clark St., Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W. Clark St., Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225","https://openalex.org/I4210135837"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111996562","display_name":"Saurabh Baheti","orcid":"https://orcid.org/0000-0002-3564-7627"},"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":"Saurabh Baheti","raw_affiliation_strings":["Mayo Clinic, Department of Research Services, 200 1st St. SW, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Department of Research Services, 200 1st St. SW, Rochester, MN, USA","institution_ids":["https://openalex.org/I4210146710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054710251","display_name":"Matthew A. Bockol","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"]},{"id":"https://openalex.org/I2802423016","display_name":"WinnMed","ror":"https://ror.org/02s47w807","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802423016"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew A Bockol","raw_affiliation_strings":["Mayo Clinic, Department of IT Executive Administration, 200 1st St. SW, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Department of IT Executive Administration, 200 1st St. SW, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723","https://openalex.org/I2802423016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016273546","display_name":"Travis Drucker","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"]},{"id":"https://openalex.org/I2802423016","display_name":"WinnMed","ror":"https://ror.org/02s47w807","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802423016"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Travis M Drucker","raw_affiliation_strings":["Mayo Clinic, Department of IT Executive Administration, 200 1st St. SW, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Department of IT Executive Administration, 200 1st St. SW, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723","https://openalex.org/I2802423016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085507659","display_name":"Steven N. Hart","orcid":"https://orcid.org/0000-0001-7714-2734"},"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":"Steven N Hart","raw_affiliation_strings":["Mayo Clinic, Department of Health Sciences Research, 200 1st St. SW, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Department of Health Sciences Research, 200 1st St. SW, Rochester, MN, USA","institution_ids":["https://openalex.org/I4210146710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024496701","display_name":"Matthew E. Hudson","orcid":"https://orcid.org/0000-0002-4737-0936"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew E Hudson","raw_affiliation_strings":["Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1102 S. Goodwin Ave., Urbana, IL, USA","Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1102 S. Goodwin Ave., Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067802693","display_name":"Ravishankar K. Iyer","orcid":"https://orcid.org/0000-0003-2245-3038"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ravishankar K Iyer","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 306 N. Wright St., Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 306 N. Wright St., Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090467582","display_name":"Michael T. Kalmbach","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"]},{"id":"https://openalex.org/I2802423016","display_name":"WinnMed","ror":"https://ror.org/02s47w807","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802423016"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael T Kalmbach","raw_affiliation_strings":["Mayo Clinic, Department of IT Executive Administration, 200 1st St. SW, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Department of IT Executive Administration, 200 1st St. SW, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723","https://openalex.org/I2802423016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017695104","display_name":"Katherine I. Kendig","orcid":null},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I4210135837","display_name":"National Center for Supercomputing Applications","ror":"https://ror.org/03r10zj06","country_code":"US","type":"facility","lineage":["https://openalex.org/I157725225","https://openalex.org/I4210135837"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katherine I Kendig","raw_affiliation_strings":["National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W. Clark St., Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W. Clark St., Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225","https://openalex.org/I4210135837"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044058635","display_name":"Eric W. Klee","orcid":"https://orcid.org/0000-0003-2946-5795"},"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":"Eric W Klee","raw_affiliation_strings":["Mayo Clinic, Department of Health Sciences Research, 200 1st St. SW, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Department of Health Sciences Research, 200 1st St. SW, Rochester, MN, USA","institution_ids":["https://openalex.org/I4210146710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061621401","display_name":"Nathan R. Mattson","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"]},{"id":"https://openalex.org/I2802423016","display_name":"WinnMed","ror":"https://ror.org/02s47w807","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802423016"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan R Mattson","raw_affiliation_strings":["Mayo Clinic, Department of IT Executive Administration, 200 1st St. SW, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Department of IT Executive Administration, 200 1st St. SW, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723","https://openalex.org/I2802423016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038929700","display_name":"Eric D. Wieben","orcid":"https://orcid.org/0000-0002-8708-0968"},"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"]},{"id":"https://openalex.org/I2802423016","display_name":"WinnMed","ror":"https://ror.org/02s47w807","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802423016"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric D Wieben","raw_affiliation_strings":["Mayo Clinic, Department of Biochemistry and Molecular Biology, 200 1st St. SW, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Department of Biochemistry and Molecular Biology, 200 1st St. SW, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723","https://openalex.org/I2802423016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034576254","display_name":"Mathieu Wiepert","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"]},{"id":"https://openalex.org/I2802423016","display_name":"WinnMed","ror":"https://ror.org/02s47w807","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802423016"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mathieu Wiepert","raw_affiliation_strings":["Mayo Clinic, Department of IT Executive Administration, 200 1st St. SW, Rochester, MN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Department of IT Executive Administration, 200 1st St. SW, Rochester, MN, USA","institution_ids":["https://openalex.org/I1330342723","https://openalex.org/I2802423016"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064052128","display_name":"Derek E. Wildman","orcid":"https://orcid.org/0000-0002-6374-5136"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Derek E Wildman","raw_affiliation_strings":["Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, 407 S. Goodwin Ave., Urbana, IL, USA","Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, 407 S. Goodwin Ave., Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032264771","display_name":"Liudmila S. Mainzer","orcid":"https://orcid.org/0000-0001-7121-0214"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I4210135837","display_name":"National Center for Supercomputing Applications","ror":"https://ror.org/03r10zj06","country_code":"US","type":"facility","lineage":["https://openalex.org/I157725225","https://openalex.org/I4210135837"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Liudmila S Mainzer","raw_affiliation_strings":["Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, USA. lmainzer@illinois.edu","National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W. Clark St., Urbana, IL, USA. lmainzer@illinois.edu","Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, USA"],"raw_orcid":"https://orcid.org/0000-0001-7121-0214","affiliations":[{"raw_affiliation_string":"Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, USA. lmainzer@illinois.edu","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 W. Clark St., Urbana, IL, USA. lmainzer@illinois.edu","institution_ids":["https://openalex.org/I4210135837"]},{"raw_affiliation_string":"Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5032264771"],"corresponding_institution_ids":["https://openalex.org/I157725225","https://openalex.org/I4210135837"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":2.8977,"has_fulltext":true,"cited_by_count":70,"citation_normalized_percentile":{"value":0.91135546,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"20","issue":"1","first_page":"557","last_page":"557"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.7627000212669373,"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":0.7627000212669373,"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":0.07509999722242355,"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":0.06599999964237213,"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/computer-science","display_name":"Computer science","score":0.8450605869293213},{"id":"https://openalex.org/keywords/spark","display_name":"SPARK (programming language)","score":0.5855719447135925},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5490579009056091},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5245499610900879},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5233415961265564},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4886837303638458},{"id":"https://openalex.org/keywords/execution-time","display_name":"Execution time","score":0.47603869438171387},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2782491445541382},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15103989839553833},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.11806485056877136}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8450605869293213},{"id":"https://openalex.org/C2781215313","wikidata":"https://www.wikidata.org/wiki/Q3493345","display_name":"SPARK (programming language)","level":2,"score":0.5855719447135925},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5490579009056091},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5245499610900879},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5233415961265564},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4886837303638458},{"id":"https://openalex.org/C2989134064","wikidata":"https://www.wikidata.org/wiki/Q288510","display_name":"Execution time","level":2,"score":0.47603869438171387},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2782491445541382},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15103989839553833},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.11806485056877136}],"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":"D002877","descriptor_name":"Chromosomes, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002877","descriptor_name":"Chromosomes, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002877","descriptor_name":"Chromosomes, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","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":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-3169-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3169-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3169-7","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:31703611","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31703611","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:d1ba367575504c22a9097a3dd969475e","is_oa":true,"landing_page_url":"https://doaj.org/article/d1ba367575504c22a9097a3dd969475e","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 20, Iss 1, Pp 1-9 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6842142","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6842142","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/s12859-019-3169-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3169-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3169-7","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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.5299999713897705}],"awards":[{"id":"https://openalex.org/G4935981367","display_name":null,"funder_award_id":"U41HG006941","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8615156336","display_name":null,"funder_award_id":"H3ABioNet","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306143","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03"},{"id":"https://openalex.org/F4320314070","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332222","display_name":"University of Illinois at Urbana-Champaign","ror":"https://ror.org/047426m28"},{"id":"https://openalex.org/F4320333659","display_name":"Center for Individualized Medicine, Mayo Clinic","ror":null},{"id":"https://openalex.org/F4320338403","display_name":"Common Fund","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2988700766.pdf","grobid_xml":"https://content.openalex.org/works/W2988700766.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W47135330","https://openalex.org/W1919257374","https://openalex.org/W2078512370","https://openalex.org/W2095680943","https://openalex.org/W2101305463","https://openalex.org/W2118526609","https://openalex.org/W2119180969","https://openalex.org/W2147733682","https://openalex.org/W2159670728","https://openalex.org/W2168133698","https://openalex.org/W2168397218","https://openalex.org/W2189371416","https://openalex.org/W2202435095","https://openalex.org/W2276632102","https://openalex.org/W2396849069","https://openalex.org/W2404609681","https://openalex.org/W2438134502","https://openalex.org/W2575651982","https://openalex.org/W2597490071","https://openalex.org/W2745359018","https://openalex.org/W2756077550","https://openalex.org/W2791837701","https://openalex.org/W2913381374","https://openalex.org/W2914183466","https://openalex.org/W3098304617","https://openalex.org/W4255955445","https://openalex.org/W4292907187"],"related_works":["https://openalex.org/W3015859229","https://openalex.org/W2230552005","https://openalex.org/W1975949872","https://openalex.org/W3159871278","https://openalex.org/W2905242764","https://openalex.org/W3109411864","https://openalex.org/W2056396287","https://openalex.org/W3195722949","https://openalex.org/W4322731236","https://openalex.org/W3009370840"],"abstract_inverted_index":{"BACKGROUND:":[0],"Use":[1],"of":[2,49,89,123,137,168,181,186,201,279,285,290,305,340,347],"the":[3,11,22,25,57,61,69,94,121,135,139,179,202,204,222,244,260,277,303,338],"Genome":[4],"Analysis":[5],"Toolkit":[6],"(GATK)":[7],"continues":[8,71],"to":[9,72,92,178,198,217,242,246,301],"be":[10,73,156,208,273,325],"standard":[12],"practice":[13],"in":[14,18,38,44,51,56,80,100,165,211],"genomic":[15],"variant":[16,142],"calling":[17,143],"both":[19,184],"research":[20],"and":[21,115,126,149,264],"clinic.":[23],"Recently":[24],"toolkit":[26],"has":[27,232],"been":[28,36],"rapidly":[29,236],"evolving.":[30],"Significant":[31],"computational":[32],"performance":[33],"improvements":[34],"have":[35],"introduced":[37],"GATK3.8":[39,125,148,257],"through":[40],"collaboration":[41],"with":[42,98,331],"Intel":[43],"2017.":[45],"The":[46,269,321],"first":[47],"release":[48],"GATK4":[50,189],"early":[52],"2018":[53],"revealed":[54],"rewrites":[55,200],"code":[58],"base,":[59],"as":[60,108],"stepping":[62],"stone":[63],"toward":[64],"a":[65,74,86,170,212,230,233,248],"Spark":[66],"implementation.":[67],"As":[68],"software":[70],"moving":[75],"target":[76],"for":[77,147,151,161,183,294],"optimal":[78],"deployment":[79],"highly":[81],"productive":[82],"environments,":[83],"we":[84,119,254,312],"present":[85],"detailed":[87],"analysis":[88,206],"these":[90],"improvements,":[91],"help":[93],"community":[95],"stay":[96],"abreast":[97],"changes":[99],"performance.":[101],"RESULTS:":[102],"We":[103,128],"re-evaluated":[104],"multiple":[105,219,267,316],"options,":[106],"such":[107,252],"threading,":[109],"parallel":[110,162],"garbage":[111],"collection,":[112],"I/O":[113],"options":[114],"data-level":[116],"parallelization.":[117],"Additionally,":[118],"considered":[120],"trade-offs":[122],"using":[124,256],"GATK4.":[127,152],"found":[129],"optimized":[130],"parameter":[131],"values":[132],"that":[133],"reduce":[134],"time":[136,167,245],"executing":[138],"best":[140],"practices":[141],"procedure":[144],"by":[145,158,258],"29.3%":[146],"16.9%":[150],"Further":[153],"speedups":[154],"can":[155,207],"accomplished":[157],"splitting":[159,259],"data":[160],"analysis,":[163],"resulting":[164],"run":[166,209],"only":[169],"few":[171],"hours":[172,275,327],"on":[173,221,281,318,328,344],"whole":[174],"human":[175],"genome":[176],"sequenced":[177],"depth":[180],"20X,":[182],"versions":[185],"GATK.":[187],"Nonetheless,":[188],"is":[190,240,299],"already":[191],"much":[192],"more":[193],"cost-effective":[194],"than":[195],"GATK3.8.":[196],"Thanks":[197],"significant":[199],"algorithms,":[203],"same":[205,223],"largely":[210],"single-threaded":[213],"fashion,":[214],"allowing":[215],"users":[216],"process":[218,247],"samples":[220,306,317,333],"CPU.":[224],"CONCLUSIONS:":[225],"In":[226,251],"time-sensitive":[227],"situations,":[228],"when":[229],"patient":[231],"critical":[234],"or":[235,293],"developing":[237],"condition,":[238],"it":[239,298],"useful":[241,300],"minimize":[243],"single":[249],"sample.":[250],"cases":[253],"recommend":[255,313],"sample":[261,343],"into":[262],"chunks":[263],"computing":[265],"across":[266],"nodes.":[268],"resultant":[270],"walltime":[271,323],"will":[272,324],"nnn.4":[274],"at":[276,337],"cost":[278,339],"$41.60":[280],"4":[282],"c5.18xlarge":[283,345],"instances":[284],"Amazon":[286,348],"Cloud.":[287,349],"For":[288],"cost-effectiveness":[289],"routine":[291],"analyses":[292],"large":[295],"population":[296],"studies,":[297],"maximize":[302],"number":[304],"processed":[307,334],"per":[308,335,342],"unit":[309],"time.":[310],"Thus":[311],"GATK4,":[314],"running":[315],"one":[319],"node.":[320],"total":[322],"\u223c34.1":[326],"40":[329],"samples,":[330],"1.18":[332],"hour":[336],"$2.60":[341],"instance":[346]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":10},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
