{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T08:10:09Z","timestamp":1772784609105,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,15]],"date-time":"2022-11-15T00:00:00Z","timestamp":1668470400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001862","name":"Formas","doi-asserted-by":"publisher","award":["2017-00453"],"award-info":[{"award-number":["2017-00453"]}],"id":[{"id":"10.13039\/501100001862","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The C++ code for prophaser is available in the GitHub repository https:\/\/github.com\/scicompuu\/prophaser.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary information is available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac738","type":"journal-article","created":{"date-parts":[[2022,11,15]],"date-time":"2022-11-15T07:49:36Z","timestamp":1668498576000},"source":"Crossref","is-referenced-by-count":17,"title":["Achieving improved accuracy for imputation of ancient\u00a0DNA"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6212-539X","authenticated-orcid":false,"given":"Kristiina","family":"Ausmees","sequence":"first","affiliation":[{"name":"Department of Information Technology, Uppsala University , Uppsala 751 05, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0458-6902","authenticated-orcid":false,"given":"Carl","family":"Nettelblad","sequence":"additional","affiliation":[{"name":"Department of Information Technology, Uppsala University , Uppsala 751 05, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,11,15]]},"reference":[{"key":"2023010107524106600_btac738-B1","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1126\/science.aay6826","article-title":"Ancient Rome: a genetic crossroads of Europe and the Mediterranean","volume":"366","author":"Antonio","year":"2019","journal-title":"Science"},{"key":"2023010107524106600_btac738-B2","doi-asserted-by":"crossref","DOI":"10.1093\/g3journal\/jkac089","article-title":"An empirical evaluation of genotype imputation of ancient DNA","volume":"12","author":"Ausmees","year":"2022","journal-title":"G3 Genes\u2014Genomes\u2014Genetics"},{"key":"2023010107524106600_btac738-B3","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"Auton","year":"2015","journal-title":"Nature"},{"key":"2023010107524106600_btac738-B4","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/j.ajhg.2015.11.020","article-title":"Genotype imputation with millions of reference samples","volume":"98","author":"Browning","year":"2016","journal-title":"Am. 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