{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T03:41:25Z","timestamp":1773373285111,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,8,25]],"date-time":"2021-08-25T00:00:00Z","timestamp":1629849600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"American Lebanese Syrian Associated Charities of St. Jude Children\u2019s Research Hospital"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Small insertions and deletions (indels) in nucleotide sequence may be represented differently between mapping algorithms and variant callers, or in the flanking sequence context. Representational ambiguity is especially profound for complex indels, complicating comparisons between multiple mappings and call sets. Complex indels may additionally suffer from incomplete allele representation, potentially leading to critical misannotation of variant effect. We present indelPost, a Python library that harmonizes these ambiguities for simple and complex indels via realignment and read-based phasing. We demonstrate that indelPost enables accurate analysis of ambiguous data and can derive the correct complex indel alleles from the simple indel predictions provided by standard small variant detectors, with improved performance over a specialized tool for complex indel analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>indelPost is freely available at: https:\/\/github.com\/stjude\/indelPost.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab601","type":"journal-article","created":{"date-parts":[[2021,8,25]],"date-time":"2021-08-25T13:51:40Z","timestamp":1629899500000},"page":"549-551","source":"Crossref","is-referenced-by-count":18,"title":["indelPost: harmonizing ambiguities in simple and complex indel alignments"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7787-2008","authenticated-orcid":false,"given":"Kohei","family":"Hagiwara","sequence":"first","affiliation":[{"name":"Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael N","family":"Edmonson","sequence":"additional","affiliation":[{"name":"Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David A","family":"Wheeler","sequence":"additional","affiliation":[{"name":"Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinghui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Computational Biology, St Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,8,25]]},"reference":[{"key":"2023020108420083000_btab601-B1","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nbt.2514","article-title":"Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples","volume":"31","author":"Cibulskis","year":"2013","journal-title":"Nat. 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