Performance evaluation of indel calling tools using real short-read data

dc.contributor.authorHasan, Mohammad Shabbiren
dc.contributor.authorWu, Xiaoweien
dc.contributor.authorZhang, Liqingen
dc.contributor.departmentComputer Scienceen
dc.contributor.departmentStatisticsen
dc.date.accessioned2017-02-02T23:06:58Zen
dc.date.available2017-02-02T23:06:58Zen
dc.date.issued2015-08-19en
dc.description.abstractBackground Insertion and deletion (indel), a common form of genetic variation, has been shown to cause or contribute to human genetic diseases and cancer. With the advance of next-generation sequencing technology, many indel calling tools have been developed; however, evaluation and comparison of these tools using large-scale real data are still scant. Here we evaluated seven popular and publicly available indel calling tools, GATK Unified Genotyper, VarScan, Pindel, SAMtools, Dindel, GTAK HaplotypeCaller, and Platypus, using 78 human genome low-coverage data from the 1000 Genomes project. Results Comparing indels called by these tools with a known set of indels, we found that Platypus outperforms other tools. In addition, a high percentage of known indels still remain undetected and the number of common indels called by all seven tools is very low. Conclusion All these findings indicate the necessity of improving the existing tools or developing new algorithms to achieve reliable and consistent indel calling results.en
dc.description.versionPublished versionen
dc.format.extent? - ? (14) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.citationHuman Genomics. 2015 Aug 19;9(1):20en
dc.identifier.doihttps://doi.org/10.1186/s40246-015-0042-2en
dc.identifier.issn1473-9542en
dc.identifier.urihttp://hdl.handle.net/10919/74910en
dc.identifier.volume9en
dc.language.isoenen
dc.publisherBiomed Centralen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000359760700001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderHasan et al.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectGenetics & Heredityen
dc.subjectIndel callingen
dc.subjectVariant callingen
dc.subjectHaplotypeCalleren
dc.subjectNext-generation sequencingen
dc.subjectDeep sequencingen
dc.subjectSoftware evaluationen
dc.subjectACUTE MYELOID-LEUKEMIAen
dc.subjectEND SHORT READSen
dc.subjectSEQUENCING DATAen
dc.subjectHUMAN GENOMEen
dc.subjectINSERTION-DELETIONen
dc.subjectGENETIC-VARIATIONen
dc.subjectCANCERen
dc.subjectVARIANTSen
dc.subjectMUTATIONSen
dc.subjectDISCOVERYen
dc.titlePerformance evaluation of indel calling tools using real short-read dataen
dc.title.serialHuman Genomicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Scienceen
pubs.organisational-group/Virginia Tech/Science/COS T&R Facultyen
pubs.organisational-group/Virginia Tech/Science/Statisticsen
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