{"id":"https://openalex.org/W2022559971","doi":"https://doi.org/10.1109/bibmw.2012.6470217","title":"Bamchop: A bioinformatics utility to summarize and visualize exome and other types of targeted resequencing data","display_name":"Bamchop: A bioinformatics utility to summarize and visualize exome and other types of targeted resequencing data","publication_year":2012,"publication_date":"2012-10-01","ids":{"openalex":"https://openalex.org/W2022559971","doi":"https://doi.org/10.1109/bibmw.2012.6470217","mag":"2022559971"},"language":"en","primary_location":{"id":"doi:10.1109/bibmw.2012.6470217","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2012.6470217","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","raw_type":"proceedings-article"},"type":"article","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/A5100443049","display_name":"Zhe Zhang","orcid":"https://orcid.org/0000-0003-3983-1226"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhe Zhang","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064934412","display_name":"Jeremy Leipzig","orcid":"https://orcid.org/0000-0001-7224-9620"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Leipzig","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043017979","display_name":"Ariella Sasson","orcid":"https://orcid.org/0000-0003-0749-507X"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ariella Sasson","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007279402","display_name":"Juan C. Per\u00edn","orcid":null},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Juan Carlos Perin","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103219447","display_name":"Michael Xie","orcid":"https://orcid.org/0000-0003-0680-8732"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Xie","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086151737","display_name":"Mahdi Sarmady","orcid":"https://orcid.org/0000-0001-6069-804X"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mahdi Sarmady","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054800561","display_name":"Patrick V. Warren","orcid":null},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patrick Warren","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101817826","display_name":"Peter S. White","orcid":"https://orcid.org/0000-0003-0313-033X"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter White","raw_affiliation_strings":["Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia City, Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]},{"raw_affiliation_string":"Center for Biomedical Informatics, The Children's Hospital of Philadelphia, City, Country Philadelphia, USA","institution_ids":["https://openalex.org/I1335321130"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5100443049"],"corresponding_institution_ids":["https://openalex.org/I1335321130"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07418527,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"670","last_page":"673"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9952999949455261,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9932000041007996,"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/exome","display_name":"Exome","score":0.6461380124092102},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6411876082420349},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.5114096999168396},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4583614766597748},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4132530689239502},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4115646481513977},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.25416332483291626},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24151891469955444},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.23496437072753906},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17381525039672852},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11427739262580872}],"concepts":[{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.6461380124092102},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6411876082420349},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.5114096999168396},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4583614766597748},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4132530689239502},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4115646481513977},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.25416332483291626},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24151891469955444},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23496437072753906},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17381525039672852},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11427739262580872}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibmw.2012.6470217","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibmw.2012.6470217","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4699999988079071,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"},{"score":0.4000000059604645,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W1994220983","https://openalex.org/W2013332287","https://openalex.org/W2036210716","https://openalex.org/W2075519390","https://openalex.org/W2108234281","https://openalex.org/W2127634492","https://openalex.org/W2160443244","https://openalex.org/W2160697532"],"related_works":["https://openalex.org/W2093932542","https://openalex.org/W4402567428","https://openalex.org/W2043256480","https://openalex.org/W2172231381","https://openalex.org/W1983406990","https://openalex.org/W2106924416","https://openalex.org/W2772505697","https://openalex.org/W3083501552","https://openalex.org/W2400191746","https://openalex.org/W2484239316"],"abstract_inverted_index":{"Targeted":[0],"resequencing":[1,74,93,165,185],"projects":[2],"can":[3],"generate":[4],"massive":[5],"amount":[6],"of":[7,12,105,143,164,190],"data":[8,55,94],"in":[9,27,32,83],"the":[10,115,131,141,148,154],"form":[11],"short":[13],"nucleic":[14,124],"acid":[15,125],"sequences.":[16],"These":[17],"sequences":[18],"are":[19],"aligned":[20],"to":[21,42,50,53,91,108,161,181],"a":[22,77,84,102,109,162,172],"reference":[23],"genome":[24],"and":[25,57,67,80,118,123,127,134,153,178],"stored":[26],"BAM":[28,46,78],"(Binary":[29],"Alignment/Map)":[30],"files":[31,47],"most":[33],"cases.":[34],"A":[35,137],"growing":[36],"challenge":[37],"for":[38,175],"biom\u00e9dical":[39],"researchers":[40],"is":[41,89,140,171,192],"rapidly":[43],"summarize":[44],"large":[45],"(typically":[48],"5":[49],"25":[51],"GB)":[52],"evaluate":[54],"quality":[56,117],"guide":[58],"follow-up":[59],"steps.":[60],"Here,":[61],"we":[62,167],"present":[63],"an":[64],"R":[65,155],"package":[66],"report":[68,139],"template,":[69],"\"bamchop\",":[70],"that":[71,95,146,169],"retrieves":[72],"targeted":[73,132],"information":[75,129],"from":[76,101,194],"file":[79],"illustrates":[81],"it":[82,160],"standardized":[85],"format.":[86],"This":[87],"program":[88],"applicable":[90],"all":[92],"investigates":[96],"selected":[97],"genomie":[98,135],"regions,":[99],"ranging":[100],"small":[103],"number":[104],"mutation":[106],"hotspots":[107],"complete":[110],"human":[111],"exome.":[112],"Bamchop":[113],"reports":[114],"sequencing":[116],"coverage,":[119],"mapping":[120],"confidence,":[121],"strand":[122],"bias,":[126],"other":[128],"about":[130],"regions":[133],"background.":[136],"bamchop":[138,170,191],"product":[142],"Sweave":[144],"framework":[145],"requires":[147],"LaTeX":[149],"document":[150],"preparation":[151],"system":[152],"statistical":[156],"environment.":[157],"In":[158],"applying":[159],"variety":[163],"projects,":[166],"determined":[168],"powerful":[173],"tool":[174],"both":[176],"bioinformaticians":[177],"bench":[179],"scientists":[180],"conveniently":[182],"assess":[183],"their":[184],"data.":[186],"The":[187],"source":[188],"code":[189],"available":[193],"https://github.com/CBMi-BiC/bamchop.":[195]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
