{"id":"https://openalex.org/W4387913722","doi":"https://doi.org/10.1109/etncc59188.2023.10284935","title":"\u201cPerformance Evaluation of Variant Calling Tools for Human and Microbial Genomes\u201d","display_name":"\u201cPerformance Evaluation of Variant Calling Tools for Human and Microbial Genomes\u201d","publication_year":2023,"publication_date":"2023-08-16","ids":{"openalex":"https://openalex.org/W4387913722","doi":"https://doi.org/10.1109/etncc59188.2023.10284935"},"language":"en","primary_location":{"id":"doi:10.1109/etncc59188.2023.10284935","doi":"https://doi.org/10.1109/etncc59188.2023.10284935","is_oa":false,"landing_page_url":"https://doi.org/10.1109/etncc59188.2023.10284935","pdf_url":null,"source":{"id":"https://openalex.org/S7407087382","display_name":"International Conference on Emerging Trends in Networks and Computer Communications (ETNCC)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 International Conference on Emerging Trends in Networks and Computer Communications (ETNCC)","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","is_traditional":true,"indexed_in":["crossref"],"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/A5078992139","display_name":"Kirti Bhadhadhara","orcid":"https://orcid.org/0009-0007-0678-3113","observed_orcids":["https://orcid.org/0009-0007-0678-3113"]},"institutions":[{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Kirti Bhadhadhara","raw_affiliation_strings":["Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India","institution_ids":["https://openalex.org/I1331500379"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021005384","display_name":"Muthukumar Balamurugan","orcid":"https://orcid.org/0009-0005-8993-1702","observed_orcids":["https://orcid.org/0009-0005-8993-1702"]},"institutions":[{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Muthukumar Balamurugan","raw_affiliation_strings":["Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India","institution_ids":["https://openalex.org/I1331500379"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053218912","display_name":"Neeraj Bharti","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Neeraj Bharti","raw_affiliation_strings":["Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India","institution_ids":["https://openalex.org/I1331500379"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029373450","display_name":"Ruma Banerjee","orcid":"https://orcid.org/0000-0001-7890-8666","observed_orcids":["https://orcid.org/0000-0001-7890-8666"]},"institutions":[{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Ruma Banerjee","raw_affiliation_strings":["Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India","institution_ids":["https://openalex.org/I1331500379"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043971144","display_name":"Sunitha Manjari Kasibhatla","orcid":"https://orcid.org/0000-0003-0320-2209","observed_orcids":["https://orcid.org/0000-0003-0320-2209"]},"institutions":[{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sunitha Manjari Kasibhatla","raw_affiliation_strings":["Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India","institution_ids":["https://openalex.org/I1331500379"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041136744","display_name":"Rajendra Joshi","orcid":"https://orcid.org/0000-0003-1299-0091","observed_orcids":["https://orcid.org/0000-0003-1299-0091"]},"institutions":[{"id":"https://openalex.org/I1331500379","display_name":"Centre for Development of Advanced Computing","ror":"https://ror.org/022abst40","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1331500379","https://openalex.org/I4210121746"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Rajendra Joshi","raw_affiliation_strings":["Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Development of Advanced Computing (C-DAC),HPC-Medical & Bioinformatics Applications Group,Pune,India","institution_ids":["https://openalex.org/I1331500379"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I1331500379"],"apc_list":null,"apc_paid":null,"fwci":1.1683,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.79235091,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":93},"biblio":{"volume":null,"issue":null,"first_page":"235","last_page":"242"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955999851226807,"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":0.9955999851226807,"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":0.00279999990016222,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.0003000000142492354,"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/variant-calling","display_name":"variant calling","score":0.9869999885559082},{"id":"https://openalex.org/keywords/variant-caller-comparison","display_name":"variant caller comparison","score":0.6290000081062317},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphisms","display_name":"single nucleotide polymorphisms","score":0.8579999804496765},{"id":"https://openalex.org/keywords/indel-calling","display_name":"indel calling","score":0.9399999976158142},{"id":"https://openalex.org/keywords/human-genome","display_name":"human genome","score":0.7540000081062317},{"id":"https://openalex.org/keywords/microbial-genomes","display_name":"microbial genomes","score":0.8059999942779541},{"id":"https://openalex.org/keywords/genome-in-a-bottle","display_name":"Genome in a Bottle","score":0.800000011920929},{"id":"https://openalex.org/keywords/bwa-mem","display_name":"BWA-MEM","score":0.9399999976158142},{"id":"https://openalex.org/keywords/bowtie2","display_name":"Bowtie2","score":0.9570000171661377},{"id":"https://openalex.org/keywords/varscan2","display_name":"VarScan2","score":0.9829999804496765},{"id":"https://openalex.org/keywords/deepvariant","display_name":"DeepVariant","score":0.9929999709129333},{"id":"https://openalex.org/keywords/freebayes","display_name":"FreeBayes","score":0.9509999752044678},{"id":"https://openalex.org/keywords/pilon","display_name":"Pilon","score":0.8349999785423279},{"id":"https://openalex.org/keywords/read-mapping","display_name":"read mapping","score":0.6499999761581421},{"id":"https://openalex.org/keywords/actionable-mutations","display_name":"actionable mutations","score":0.593999981880188},{"id":"https://openalex.org/keywords/false-positive-reduction","display_name":"false positive reduction","score":0.5789999961853027}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.8514478802680969},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.7700798511505127},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6641817688941956},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6390622854232788},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.6222959160804749},{"id":"https://openalex.org/C112789634","wikidata":"https://www.wikidata.org/wiki/Q18207010","display_name":"False positives and false negatives","level":3,"score":0.6088495850563049},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.571325421333313},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.5103604197502136},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5054669380187988},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4832378327846527},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.47748610377311707},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.44056397676467896},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3922804594039917},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.37722674012184143},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3336624503135681},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3176993131637573},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3134719133377075},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15366101264953613},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.07520893216133118},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/etncc59188.2023.10284935","doi":"https://doi.org/10.1109/etncc59188.2023.10284935","is_oa":false,"landing_page_url":"https://doi.org/10.1109/etncc59188.2023.10284935","pdf_url":null,"source":{"id":"https://openalex.org/S7407087382","display_name":"International Conference on Emerging Trends in Networks and Computer Communications (ETNCC)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 International Conference on Emerging Trends in Networks and Computer Communications (ETNCC)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320325255","display_name":"Ministry of Electronics and Information technology","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":77,"referenced_works":["https://openalex.org/W1579111454","https://openalex.org/W1596062789","https://openalex.org/W1604187205","https://openalex.org/W1659211059","https://openalex.org/W1919257374","https://openalex.org/W1964807436","https://openalex.org/W1967296216","https://openalex.org/W1969802281","https://openalex.org/W1973679647","https://openalex.org/W1975345997","https://openalex.org/W1982703709","https://openalex.org/W1982855075","https://openalex.org/W1983426138","https://openalex.org/W1984259444","https://openalex.org/W1985722159","https://openalex.org/W1993945142","https://openalex.org/W1996792558","https://openalex.org/W2005271647","https://openalex.org/W2015831381","https://openalex.org/W2029964106","https://openalex.org/W2032046925","https://openalex.org/W2034132675","https://openalex.org/W2036933725","https://openalex.org/W2039694241","https://openalex.org/W2050109119","https://openalex.org/W2061596350","https://openalex.org/W2068146190","https://openalex.org/W2076398093","https://openalex.org/W2080347313","https://openalex.org/W2091193685","https://openalex.org/W2091264144","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2104816742","https://openalex.org/W2108066473","https://openalex.org/W2108234281","https://openalex.org/W2116041602","https://openalex.org/W2132846849","https://openalex.org/W2144594443","https://openalex.org/W2150131459","https://openalex.org/W2153805608","https://openalex.org/W2155943701","https://openalex.org/W2158217645","https://openalex.org/W2158322625","https://openalex.org/W2158336776","https://openalex.org/W2158714788","https://openalex.org/W2168019567","https://openalex.org/W2168783124","https://openalex.org/W2170551349","https://openalex.org/W2172139908","https://openalex.org/W2174623150","https://openalex.org/W2189510244","https://openalex.org/W2190569576","https://openalex.org/W2263875137","https://openalex.org/W2312526538","https://openalex.org/W2417483443","https://openalex.org/W2482598544","https://openalex.org/W2561512876","https://openalex.org/W2582849274","https://openalex.org/W2584732844","https://openalex.org/W2589069466","https://openalex.org/W2598066557","https://openalex.org/W2614575602","https://openalex.org/W2625348030","https://openalex.org/W2740414557","https://openalex.org/W2770779826","https://openalex.org/W2795930404","https://openalex.org/W2889664156","https://openalex.org/W2929354011","https://openalex.org/W2936667766","https://openalex.org/W2951331911","https://openalex.org/W2951775202","https://openalex.org/W3005014603","https://openalex.org/W3014638255","https://openalex.org/W3188556937","https://openalex.org/W6749655863","https://openalex.org/W7099578761"],"related_works":["https://openalex.org/W4225764874","https://openalex.org/W7015238468","https://openalex.org/W2190569576","https://openalex.org/W3160731134","https://openalex.org/W7128041901","https://openalex.org/W4210932301","https://openalex.org/W2949462305","https://openalex.org/W2972952311","https://openalex.org/W3101579057","https://openalex.org/W1579111454"],"abstract_inverted_index":{"Analyzing":[0],"the":[1,58,138,144,162,231],"data":[2,252],"deluge":[3],"generated":[4],"by":[5,94,130,247],"next":[6],"generation":[7],"sequencing":[8],"technologies":[9],"is":[10,28],"a":[11,66,234],"challenging":[12],"task.":[13],"Variant":[14,69,166,206],"calling":[15,33,70,96,135,164,167,207,224],"aids":[16],"in":[17,36,65,112,137,255],"characterizing":[18],"phenotype":[19],"of":[20,25,38,63,114,161,183,258,265,278],"an":[21],"organism.":[22],"The":[23,107],"objective":[24],"this":[26,269],"work":[27],"to":[29,147,273],"compare":[30],"popular":[31,47,75],"variant":[32,76,95,134,163,241],"protocols":[34],"available":[35],"terms":[37,113],"their":[39],"accuracy":[40],"for":[41,57,90,126,158,171,188,216,240,276],"human":[42,59,191],"and":[43,53,82,105,119,154,204,211,268],"microbial":[44,85,218],"genomes.":[45],"Three":[46],"read":[48,172],"aligners":[49],"viz.":[50,78],"BWA-MEM,":[51],"Bowtie2":[52],"NovoAlign":[54],"were":[55,110,156,245],"used":[56,89,125],"genome":[60],"benchmark":[61],"dataset":[62,141],"Genome":[64],"Bottle":[67],"(GIAB).":[68],"was":[71,88,124,200,228,236],"performed":[72],"using":[73,97,169,208],"four":[74],"callers":[77],"samtools-bcftools,":[79],"VarScan2,":[80],"GATK-HC":[81,196,212],"DeepVariant.":[83],"For":[84,193],"genomes,":[86],"BWA-MEM":[87,170],"reference":[91],"mapping":[92,173],"followed":[93],"above-mentioned":[98],"tools":[99],"(excluding":[100],"DeepVariant)":[101],"along":[102,174],"with":[103,175,197,213,225,249],"FreeBayes":[104],"PILON.":[106],"predicted":[108,180],"variants":[109,244],"assessed":[111],"true":[115,151],"positives,":[116],"false":[117,120,139,266],"positives":[118,267],"negatives.":[121],"Consensus":[122],"approach":[123,270],"identifying":[127],"SNPs":[128],"(predicted":[129],"more":[131],"than":[132],"one":[133],"pipeline)":[136],"positive":[140],"that":[142],"satisfied":[143],"threshold":[145],"criteria":[146],"be":[148,274],"included":[149],"as":[150],"positives.":[152],"Precision":[153],"Recall":[155],"measured":[157],"evaluating":[159],"each":[160],"pipelines.":[165],"pipeline":[168],"either":[176],"VarScan2":[177,203],"or":[178],"samtools-bcftools":[179],"optimal":[181,221],"number":[182],"single":[184],"nucleotide":[185],"polymorphisms":[186],"(SNP)":[187],"high":[189,260],"coverage":[190],"datasets.":[192],"Indel":[194],"calling,":[195],"any":[198],"aligner":[199],"preferred":[201],"over":[202],"samtools-bcftools.":[205],"bcftools,":[209],"Pilon":[210],"default":[214],"parameters":[215],"heterogeneous":[217],"datasets":[219],"revealed":[220],"performance.":[222],"SNP":[223],"minimum":[226],"errors":[227],"evident":[229],"when$\\sim\\mathbf{95}\\%$of":[230],"samples":[232],"from":[233],"population":[235],"taken":[237],"into":[238],"cognizance":[239],"prediction.":[242],"Predicted":[243],"validated":[246],"comparing":[248],"gold":[250],"standard":[251],"which":[253],"aided":[254],"improved":[256],"identification":[257],"actionable":[259,279],"confidence":[261],"variants,":[262],"reduced":[263],"prediction":[264],"has":[271],"proved":[272],"valuable":[275],"prioritization":[277],"variants.":[280]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2023-10-25T00:00:00"}