{"id":"https://openalex.org/W3197134032","doi":"https://doi.org/10.1093/bioinformatics/btab606","title":"Custom workflows to improve joint variant calling from multiple related tumour samples: FreeBayesSomatic and Strelka2Pass","display_name":"Custom workflows to improve joint variant calling from multiple related tumour samples: FreeBayesSomatic and Strelka2Pass","publication_year":2021,"publication_date":"2021-09-01","ids":{"openalex":"https://openalex.org/W3197134032","doi":"https://doi.org/10.1093/bioinformatics/btab606","mag":"3197134032"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab606","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab606","pdf_url":null,"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"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003728019","display_name":"Sebastian Hollizeck","orcid":"https://orcid.org/0000-0002-9504-3497"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"S Hollizeck","raw_affiliation_strings":["Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3000, Australia"],"affiliations":[{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584","https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057287263","display_name":"Stephen Q. Wong","orcid":"https://orcid.org/0000-0002-7335-2168"},"institutions":[{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]},{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"S Q Wong","raw_affiliation_strings":["Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3000, Australia"],"affiliations":[{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584","https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045959942","display_name":"Benjamin Solomon","orcid":"https://orcid.org/0000-0003-3059-5730"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"B Solomon","raw_affiliation_strings":["Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3000, Australia"],"affiliations":[{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584","https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064411888","display_name":"Dineika Chandrananda","orcid":"https://orcid.org/0000-0002-8834-9500"},"institutions":[{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]},{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"D Chandrananda","raw_affiliation_strings":["Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3000, Australia"],"affiliations":[{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584","https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090666071","display_name":"Sarah\u2010Jane Dawson","orcid":"https://orcid.org/0000-0002-8276-0374"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I2800555584","display_name":"Peter MacCallum Cancer Centre","ror":"https://ror.org/02a8bt934","country_code":"AU","type":"healthcare","lineage":["https://openalex.org/I2800555584"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"S-J Dawson","raw_affiliation_strings":["Centre for Cancer Research, University of Melbourne , Melbourne, VIC 3000, Australia","Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3000, Australia"],"affiliations":[{"raw_affiliation_string":"Centre for Cancer Research, University of Melbourne , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Peter MacCallum Cancer Centre , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584"]},{"raw_affiliation_string":"Sir Peter MacCallum Department of Oncology, University of Melbourne , Melbourne, VIC 3000, Australia","institution_ids":["https://openalex.org/I2800555584","https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5064411888","https://openalex.org/A5090666071"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I2800555584"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.09712083,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"37","issue":"21","first_page":"3916","last_page":"3919"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9986000061035156,"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":0.9986000061035156,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9915000200271606,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9865999817848206,"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/executable","display_name":"Executable","score":0.856279730796814},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7905068397521973},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7152175903320312},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6175222992897034},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.4656409025192261},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4532705843448639},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44408655166625977},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3319520354270935},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.18199479579925537}],"concepts":[{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.856279730796814},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7905068397521973},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7152175903320312},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6175222992897034},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.4656409025192261},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4532705843448639},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44408655166625977},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3319520354270935},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.18199479579925537},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btab606","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab606","pdf_url":null,"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"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G1083765528","display_name":null,"funder_award_id":"1173450","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G1365415064","display_name":null,"funder_award_id":"19002","funder_id":"https://openalex.org/F4320310187","funder_display_name":"Victorian Cancer Agency"},{"id":"https://openalex.org/G2470132094","display_name":null,"funder_award_id":"19008","funder_id":"https://openalex.org/F4320310187","funder_display_name":"Victorian Cancer Agency"},{"id":"https://openalex.org/G5409725804","display_name":null,"funder_award_id":"1194783","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G6559960980","display_name":null,"funder_award_id":"1196755","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G8586320608","display_name":null,"funder_award_id":"1158345","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320310187","display_name":"Victorian Cancer Agency","ror":"https://ror.org/0316wrd42"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1565378970","https://openalex.org/W1905089044","https://openalex.org/W2139838486","https://openalex.org/W2152956782","https://openalex.org/W2157539385","https://openalex.org/W2168133698","https://openalex.org/W2791294221","https://openalex.org/W2867868648","https://openalex.org/W2896930952","https://openalex.org/W2899285497","https://openalex.org/W2950945543","https://openalex.org/W2990871782","https://openalex.org/W3000979489","https://openalex.org/W3005774532","https://openalex.org/W3006716981","https://openalex.org/W3134688004","https://openalex.org/W6771040913"],"related_works":["https://openalex.org/W82161441","https://openalex.org/W1576042299","https://openalex.org/W1990602094","https://openalex.org/W2181943964","https://openalex.org/W1528423264","https://openalex.org/W2598672065","https://openalex.org/W3120610872","https://openalex.org/W1638297612","https://openalex.org/W2523911541","https://openalex.org/W2113128227"],"abstract_inverted_index":{"Abstract":[0],"Summary":[1],"This":[2],"work":[3],"describes":[4],"two":[5],"novel":[6],"workflows":[7,39],"for":[8],"variant":[9],"calling":[10],"that":[11,37],"extend":[12],"the":[13,66,76],"widely":[14],"used":[15],"algorithms":[16],"of":[17],"Strelka2":[18],"and":[19,30,43,54,59,70],"FreeBayes":[20],"to":[21],"call":[22],"somatic":[23],"mutations":[24],"from":[25],"multiple":[26],"related":[27],"tumour":[28],"samples":[29],"one":[31],"matched":[32],"normal":[33],"sample.":[34],"We":[35],"show":[36],"these":[38],"offer":[40],"higher":[41],"precision":[42],"recall":[44],"than":[45],"their":[46],"single":[47],"tumour-normal":[48],"pair":[49],"equivalents":[50],"in":[51],"both":[52],"simulated":[53],"clinical":[55],"sequencing":[56],"data.":[57],"Availability":[58],"implementation":[60],"Source":[61],"code":[62],"freely":[63],"available":[64,84],"at":[65,85],"following":[67],"link:":[68],"https://atlassian.petermac.org.au/bitbucket/projects/DAW/repos/multisamplevariantcalling":[69],"executable":[71],"through":[72],"Janis":[73],"(https://github.com/PMCC-BioinformaticsCore/janis)":[74],"under":[75],"GPLv3":[77],"licence.":[78],"Supplementary":[79,81],"information":[80],"data":[82],"are":[83],"Bioinformatics":[86],"online.":[87]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2021-09-13T00:00:00"}
