{"id":"https://openalex.org/W7201864029","doi":"https://doi.org/10.46471/gigabyte.194","title":"vardictcpp: a C++ reimplementation of VarDict variant caller","display_name":"vardictcpp: a C++ reimplementation of VarDict variant caller","publication_year":2026,"publication_date":"2026-10-20","ids":{"openalex":"https://openalex.org/W7201864029","doi":"https://doi.org/10.46471/gigabyte.194","pmid":"https://pubmed.ncbi.nlm.nih.gov/42964349","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13720296"},"language":"en","primary_location":{"id":"doi:10.46471/gigabyte.194","doi":"https://doi.org/10.46471/gigabyte.194","is_oa":true,"landing_page_url":"https://doi.org/10.46471/gigabyte.194","pdf_url":"https://gigabytejournal.com/admin/apis/public/article_shell/uploads/article_files/Gigabyte/Gigabyte/2026/gigabyte194/gigabyte194.pdf","source":{"id":"https://openalex.org/S4210239740","display_name":"Gigabyte","issn_l":"2709-4715","issn":["2709-4715"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","norway-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Gigabyte","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://gigabytejournal.com/admin/apis/public/article_shell/uploads/article_files/Gigabyte/Gigabyte/2026/gigabyte194/gigabyte194.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Joachim Wolff","orcid":"https://orcid.org/0000-0001-9985-955X","observed_orcids":["https://orcid.org/0000-0001-9985-955X"]},"institutions":[{"id":"https://openalex.org/I34809795","display_name":"Medizinische Hochschule Hannover","ror":"https://ror.org/00f2yqf98","country_code":"DE","type":"education","lineage":["https://openalex.org/I34809795"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Joachim Wolff","raw_affiliation_strings":["Hannover Medical School"],"raw_orcid":"https://orcid.org/0000-0001-9985-955X","affiliations":[{"raw_affiliation_string":"Hannover Medical School","institution_ids":["https://openalex.org/I34809795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I34809795"],"apc_list":{"value":350,"currency":"USD","value_usd":350},"apc_paid":{"value":350,"currency":"USD","value_usd":350},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.47758402,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2026","issue":null,"first_page":"gigabyte194","last_page":"gigabyte194"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9185000061988831,"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":0.9185000061988831,"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":0.06710000336170197,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.005900000222027302,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/variant-calling","display_name":"variant calling","score":0.7900000214576721},{"id":"https://openalex.org/keywords/somatic-mutations","display_name":"somatic mutations","score":0.7730000019073486},{"id":"https://openalex.org/keywords/jak2-v617f-mutation","display_name":"JAK2 V617F mutation","score":0.9739999771118164},{"id":"https://openalex.org/keywords/myeloid-neoplasms","display_name":"myeloid neoplasms","score":0.9980000257492065},{"id":"https://openalex.org/keywords/whole-exome-sequencing","display_name":"exome sequencing","score":0.8220000267028809},{"id":"https://openalex.org/keywords/computational-performance","display_name":"computational performance","score":0.5189999938011169},{"id":"https://openalex.org/keywords/memory-usage","display_name":"memory usage","score":0.9259999990463257},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"parallel computing","score":0.4819999933242798}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6140999794006348},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4715000092983246},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4564000070095062},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37389999628067017},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.31790000200271606},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2809000015258789},{"id":"https://openalex.org/C133462117","wikidata":"https://www.wikidata.org/wiki/Q4929239","display_name":"Data collection","level":2,"score":0.2770000100135803},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.27239999175071716},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.2718999981880188},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2687000036239624},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2628999948501587}],"mesh":[],"locations_count":8,"locations":[{"id":"doi:10.46471/gigabyte.194","doi":"https://doi.org/10.46471/gigabyte.194","is_oa":true,"landing_page_url":"https://doi.org/10.46471/gigabyte.194","pdf_url":"https://gigabytejournal.com/admin/apis/public/article_shell/uploads/article_files/Gigabyte/Gigabyte/2026/gigabyte194/gigabyte194.pdf","source":{"id":"https://openalex.org/S4210239740","display_name":"Gigabyte","issn_l":"2709-4715","issn":["2709-4715"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","norway-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Gigabyte","raw_type":"journal-article"},{"id":"doi:10.64898/2026.09.23.753771","doi":"https://doi.org/10.64898/2026.09.23.753771","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.23.753771","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.23.753771.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:13720296","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13720296/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13720296/pdf/gigabyte-2026-194.pdf","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"GigaByte","raw_type":"Text"},{"id":"pmid:42964349","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42964349","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,"listed_in":[],"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":"GigaByte (Hong Kong, China)","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:c29551eb102b4351923596d11993af83","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/c29551eb102b4351923596d11993af83","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,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"GigaByte (2026)","raw_type":"article"},{"id":"doi:10.5281/zenodo.21836658","doi":"https://doi.org/10.5281/zenodo.21836658","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.21836658","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"doi:10.5281/zenodo.21836659","doi":"https://doi.org/10.5281/zenodo.21836659","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.21836659","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"doi:10.5281/zenodo.22955424","doi":"https://doi.org/10.5281/zenodo.22955424","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22955424","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"doi:10.46471/gigabyte.194","doi":"https://doi.org/10.46471/gigabyte.194","is_oa":true,"landing_page_url":"https://doi.org/10.46471/gigabyte.194","pdf_url":"https://gigabytejournal.com/admin/apis/public/article_shell/uploads/article_files/Gigabyte/Gigabyte/2026/gigabyte194/gigabyte194.pdf","source":{"id":"https://openalex.org/S4210239740","display_name":"Gigabyte","issn_l":"2709-4715","issn":["2709-4715"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-d","norway-1"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Gigabyte","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7201864029.pdf","grobid_xml":"https://content.openalex.org/works/W7201864029.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1964807436","https://openalex.org/W2043398720","https://openalex.org/W2323851578","https://openalex.org/W2944727022","https://openalex.org/W2990871782","https://openalex.org/W3147574308","https://openalex.org/W4307711549","https://openalex.org/W4399806860","https://openalex.org/W4417153283","https://openalex.org/W7116113578"],"related_works":["https://openalex.org/W4391262162","https://openalex.org/W2899785375","https://openalex.org/W4205414581","https://openalex.org/W4415368650","https://openalex.org/W2919665556","https://openalex.org/W4309400727","https://openalex.org/W4407057918","https://openalex.org/W7136089310","https://openalex.org/W2309423881","https://openalex.org/W7208808964"],"abstract_inverted_index":{"Genomic":[0],"variant":[1,39],"calling":[2],"is":[3,99,153,165],"a":[4,60,84,90],"central":[5],"computational":[6],"task":[7],"in":[8,24,30,41,81,96,104,167],"disease":[9],"research":[10],"and":[11,32,107,147,169],"diagnostics,":[12],"where":[13],"somatic":[14],"mutations":[15],"such":[16],"as":[17,21],"JAK2":[18],"V617F":[19],"serve":[20],"diagnostic":[22],"markers":[23],"myeloid":[25],"neoplasms.":[26],"VarDict,":[27],"originally":[28],"written":[29],"Perl,":[31],"its":[33],"reimplementation":[34,93],"VarDictJava":[35,56,95,130],"are":[36,125],"widely":[37],"used":[38],"callers":[40],"the":[42,73,132],"bioinformatics":[43],"community.":[44],"The":[45,136],"Perl":[46],"implementation":[47],"requires":[48],"run":[49,80],"times":[50,102,109,119],"of":[51,68,75,94,129],"up":[52,116],"to":[53,59,117,127],"several":[54],"hours;":[55],"reduces":[57],"this":[58],"few":[61],"minutes":[62],"but":[63],"can":[64,78],"consume":[65],"large":[66],"amounts":[67],"main":[69,121],"memory,":[70],"which":[71,152],"limits":[72],"number":[74],"jobs":[76,143],"that":[77],"be":[79],"parallel":[82],"on":[83,131,144],"given":[85],"machine.":[86],"We":[87],"present":[88],"vardictcpp,":[89],"functionally":[91],"identical":[92,126],"C++17.":[97],"vardictcpp":[98,164],"approximately":[100],"four":[101],"faster":[103,110],"single-core":[105],"execution":[106],"9-11":[108],"using":[111],"eight":[112],"cores,":[113],"while":[114],"requiring":[115],"17":[118],"less":[120],"memory.":[122],"Variant":[123],"calls":[124],"those":[128],"evaluated":[133],"whole-exome":[134],"samples.":[135],"reduced":[137],"memory":[138],"footprint":[139],"allows":[140],"more":[141],"concurrent":[142],"existing":[145],"hardware":[146],"thereby":[148],"increases":[149],"sample":[150],"throughput,":[151],"particularly":[154],"relevant":[155],"for":[156],"clinical":[157],"sequencing":[158],"laboratories":[159],"with":[160],"fixed":[161],"compute":[162],"resources.":[163],"implemented":[166],"C++17":[168],"freely":[170],"available":[171],"at":[172],"https://github.com/MHH-Bioinformatics-Hematology/vardictcpp.":[173]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-08-08T00:00:00"}