{"id":"https://openalex.org/W2145636602","doi":"https://doi.org/10.1093/bioinformatics/btq092","title":"High quality SNP calling using Illumina data at shallow coverage","display_name":"High quality SNP calling using Illumina data at shallow coverage","publication_year":2010,"publication_date":"2010-02-26","ids":{"openalex":"https://openalex.org/W2145636602","doi":"https://doi.org/10.1093/bioinformatics/btq092","mag":"2145636602","pmid":"https://pubmed.ncbi.nlm.nih.gov/20190250"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq092","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq092","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","pubmed"],"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/A5013572921","display_name":"Nawar Malhis","orcid":"https://orcid.org/0000-0002-1317-833X"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Nawar Malhis","raw_affiliation_strings":["Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada"],"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada","institution_ids":["https://openalex.org/I1289530486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100728059","display_name":"Steven J.M. Jones","orcid":"https://orcid.org/0000-0003-3394-2208"},"institutions":[{"id":"https://openalex.org/I1289530486","display_name":"BC Cancer Agency","ror":"https://ror.org/03sfybe47","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1289530486"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Steven J. M. Jones","raw_affiliation_strings":["Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada"],"affiliations":[{"raw_affiliation_string":"Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada","institution_ids":["https://openalex.org/I1289530486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5013572921"],"corresponding_institution_ids":["https://openalex.org/I1289530486"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.7008,"has_fulltext":false,"cited_by_count":55,"citation_normalized_percentile":{"value":0.93913823,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"26","issue":"8","first_page":"1029","last_page":"1035"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.998199999332428,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9918000102043152,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.7549663186073303},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.6283764243125916},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5237805247306824},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5050836205482483},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.49730756878852844},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4928903579711914},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4028235673904419},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.359366774559021},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3340049684047699},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3278878927230835},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20227110385894775},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.11108314990997314}],"concepts":[{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.7549663186073303},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.6283764243125916},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5237805247306824},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5050836205482483},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.49730756878852844},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4928903579711914},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4028235673904419},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.359366774559021},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3340049684047699},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3278878927230835},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20227110385894775},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.11108314990997314},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btq092","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq092","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"},{"id":"pmid:20190250","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20190250","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1528782506","https://openalex.org/W2004834404","https://openalex.org/W2072193858","https://openalex.org/W2097341408","https://openalex.org/W2103441770","https://openalex.org/W2106808791","https://openalex.org/W2108234281","https://openalex.org/W2112113834","https://openalex.org/W2124985265","https://openalex.org/W2143124024","https://openalex.org/W2166621589"],"related_works":["https://openalex.org/W1517693310","https://openalex.org/W2327017833","https://openalex.org/W2107417504","https://openalex.org/W860817473","https://openalex.org/W2379353909","https://openalex.org/W1901150897","https://openalex.org/W2084659082","https://openalex.org/W1966708416","https://openalex.org/W1199774223","https://openalex.org/W2145432896"],"abstract_inverted_index":{"Detection":[0],"of":[1,39,66,95,120,126,142],"single":[2,24],"nucleotide":[3],"polymorphisms":[4],"(SNPs)":[5],"has":[6],"been":[7],"a":[8,28,32,40,127],"major":[9],"application":[10],"in":[11,132,152],"processing":[12],"second":[13],"generation":[14],"sequencing":[15,54],"(SGS)":[16],"data.":[17,73],"In":[18,74,103],"principle,":[19],"SNPs":[20,68,97,125,136,146,149],"are":[21],"called":[22,67,96],"on":[23,63],"base":[25],"differences":[26],"between":[27],"reference":[29,57],"genome":[30,58],"and":[31,83,109,135,147,150],"sequence":[33],"generated":[34],"from":[35,48],"SGS":[36],"short":[37],"reads":[38],"sample":[41],"genome.":[42],"However,":[43],"this":[44,75],"exercise":[45],"is":[46,118],"far":[47],"trivial;":[49],"several":[50],"parameters":[51],"related":[52],"to":[53,105,138],"quality,":[55],"and/or":[56],"properties,":[59],"play":[60],"essential":[61],"effect":[62],"the":[64,106,133],"accuracy":[65],"especially":[69],"at":[70],"shallow":[71],"coverage":[72],"work,":[76],"we":[77],"present":[78],"Slider":[79,116],"II,":[80],"an":[81,113],"alignment":[82,108,134],"SNP":[84,110],"calling":[85,137],"approach":[86],"that":[87],"demonstrates":[88],"improved":[89],"algorithmic":[90],"approaches":[91],"enabling":[92],"larger":[93],"number":[94],"with":[98],"lower":[99],"false":[100],"positive":[101],"rate.":[102],"addition":[104],"regular":[107],"calling,":[111],"as":[112,130],"optional":[114],"feature,":[115],"II":[117],"capable":[119],"utilizing":[121],"information":[122],"about":[123],"known":[124,145],"target":[128],"genome,":[129],"priors,":[131],"enhance":[139],"it's":[140],"capability":[141],"detecting":[143],"these":[144],"novel":[148],"mutations":[151],"their":[153],"vicinity.":[154]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":9}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
