{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T02:29:48Z","timestamp":1722738588913},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Recent studies sequenced tumor samples from the same progenitor at different development stages and showed that by taking into account the phylogeny of this development, single-nucleotide variant (SNV) calling can be improved. Accurate SNV calls can better reveal early-stage tumors, identify mechanisms of cancer progression or help in drug targeting.<\/jats:p>\n               <jats:p>Results: We present SNV-PPILP, a fast and easy to use tool for refining GATK\u2019s Unified Genotyper SNV calls, for multiple samples assumed to form a phylogeny. We tested SNV-PPILP on simulated data, with a varying number of samples, SNVs, read coverage and violations of the perfect phylogeny assumption. We always match or improve the accuracy of GATK, with a significant improvement on low read coverage.<\/jats:p>\n               <jats:p>Availability and implementation: SNV-PPILP, available at cs.helsinki.fi\/gsa\/snv-ppilp\/, is written in Python and requires the free ILP solver lp_solve.<\/jats:p>\n               <jats:p>Contact: \u00a0tomescu@cs.helsinki.fi<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu755","type":"journal-article","created":{"date-parts":[[2014,11,15]],"date-time":"2014-11-15T04:10:48Z","timestamp":1416024648000},"page":"1133-1135","source":"Crossref","is-referenced-by-count":11,"title":["SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP"],"prefix":"10.1093","volume":"31","author":[{"given":"Karen E.","family":"van Rens","sequence":"first","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and 2HAN University of Applied Sciences, Nijmegen, The Netherlands"},{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and 2HAN University of Applied Sciences, Nijmegen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Veli","family":"M\u00e4kinen","sequence":"additional","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and 2HAN University of Applied Sciences, Nijmegen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandru I.","family":"Tomescu","sequence":"additional","affiliation":[{"name":"1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and 2HAN University of Applied Sciences, Nijmegen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,11,13]]},"reference":[{"key":"2023051309143355300_btu755-B1","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/0025-5564(75)90040-1","article-title":"An idealized concept of the true cladistic character","volume":"23","author":"Estabrook","year":"1975","journal-title":"Math. 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