{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T17:17:56Z","timestamp":1790788676115,"version":"4.1.0"},"reference-count":29,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2020,3,23]],"date-time":"2020-03-23T00:00:00Z","timestamp":1584921600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1126157"],"award-info":[{"award-number":["GNT1126157"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns4:p>\n                    <ns4:bold>Background:<\/ns4:bold>\n                    Short tandem repeats are an important source of genetic variation. They are highly mutable and repeat expansions are associated dozens of human disorders, such as Huntington's disease and spinocerebellar ataxias. Technical advantages in sequencing technology have made it possible to analyse these repeats at large scale; however, accurate genotyping is still a challenging task. We compared four different short tandem repeats genotyping tools on whole exome sequencing data to determine their genotyping performance and limits, which will aid other researchers in choosing a suitable tool and parameters for analysis.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods:<\/ns4:bold>\n                    The analysis was performed on the Simons Simplex Collection dataset, where we used a novel method of evaluation with accuracy determined by the rate of homozygous calls on the X chromosome of male samples. In total we analysed 433 samples and around a million genotypes for evaluating tools on whole exome sequencing data.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Results:<\/ns4:bold>\n                    We determined a relatively good performance of all tools when genotyping repeats of 3-6 bp in length, which could be improved with coverage and quality score filtering. However, genotyping homopolymers was challenging for all tools and a high error rate was present across different thresholds of coverage and quality scores. Interestingly, dinucleotide repeats displayed a high error rate as well, which was found to be mainly caused by the AC\/TG repeats. Overall, LobSTR was able to make the most calls and was also the fastest tool, while RepeatSeq and HipSTR exhibited the lowest heterozygous error rate at low coverage.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusions:<\/ns4:bold>\n                    All tools have different strengths and weaknesses and the choice may depend on the application. In this analysis we demonstrated the effect of using different filtering parameters and offered recommendations based on the trade-off between the best accuracy of genotyping and the highest number of calls.\n                  <\/ns4:p>","DOI":"10.12688\/f1000research.22639.1","type":"journal-article","created":{"date-parts":[[2020,3,23]],"date-time":"2020-03-23T04:50:07Z","timestamp":1584939007000},"page":"200","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":34,"title":["Accuracy of short tandem repeats genotyping tools in whole exome sequencing data"],"prefix":"10.12688","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5248-4121","authenticated-orcid":false,"given":"Andreas","family":"Halman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9788-5690","authenticated-orcid":false,"given":"Alicia","family":"Oshlack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2020,3,23]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"573-80","DOI":"10.1093\/nar\/27.2.573","article-title":"Tandem repeats finder: a program to analyze DNA sequences.","volume":"27","author":"G Benson","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"ref-2","article-title":"Comparison of Variant Calls from Whole Genome and Whole Exome Sequencing Data Using Matched Samples.","volume":"5","author":"N 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.24995.r61590, Elizabeth A. Worthey, Center for Computational Genomics and Data Science, Departments of Pediatrics and Pathology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA, 26 May 2020, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/9-200\/v1#referee-response-61590","order":0,"name":"referee-response-61590","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.24995.r63745, Jan Radvanszky, Jaroslav Budi\u0161, Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia, 17 Jun 2020, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/9-200\/v1#referee-response-63745","order":1,"name":"referee-response-63745","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.24995.r63748, Maria Anisimova, Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Waedenswil, Switzerland, 30 Jun 2020, version 1, indexed","URL":"https:\/\/f1000research.com\/articles\/9-200\/v1#referee-response-63748","order":2,"name":"referee-response-63748","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"A.O. is supported by an NHMRC fellowship [GNT1126157]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}