{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T07:28:43Z","timestamp":1772522923420,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2017,9,18]],"date-time":"2017-09-18T00:00:00Z","timestamp":1505692800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31701415 and 91435204"],"award-info":[{"award-number":["31701415 and 91435204"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>DNA methylation is important for gene silencing and imprinting in both plants and animals. Recent advances in bisulfite sequencing allow detection of single nucleotide variations (SNVs) achieving high sensitivity, but accurately identifying heterozygous SNVs from partially C-to-T converted sequences remains challenging.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We designed two methods, BayesWC and BinomWC, that substantially improved the precision of heterozygous SNV calls from \u223c80% to 99% while retaining comparable recalls. With these SNV calls, we provided functions for allele-specific DNA methylation (ASM) analysis and visualizing the methylation status on reads. Applying ASM analysis to a previous dataset, we found that an average of 1.5% of investigated regions showed allelic methylation, which were significantly enriched in transposon elements and likely to be shared by the same cell-type. A dynamic fragment strategy was utilized for DMR analysis in low-coverage data and was able to find differentially methylated regions (DMRs) related to key genes involved in tumorigenesis using a public cancer dataset. Finally, we integrated 40 applications into the software package CGmapTools to analyze DNA methylomes. This package uses CGmap as the format interface, and designs binary formats to reduce the file size and support fast data retrieval, and can be applied for context-wise, gene-wise, bin-wise, region-wise and sample-wise analyses and visualizations.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The CGmapTools software is freely available at https:\/\/cgmaptools.github.io\/.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx595","type":"journal-article","created":{"date-parts":[[2017,9,15]],"date-time":"2017-09-15T19:13:59Z","timestamp":1505502839000},"page":"381-387","source":"Crossref","is-referenced-by-count":184,"title":["CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5199-1359","authenticated-orcid":false,"given":"Weilong","family":"Guo","sequence":"first","affiliation":[{"name":"State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China"}]},{"given":"Ping","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China"},{"name":"BIOPIC, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, China"}]},{"given":"Matteo","family":"Pellegrini","sequence":"additional","affiliation":[{"name":"Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA"}]},{"given":"Michael Q","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, USA"},{"name":"Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, Beijing, China"}]},{"given":"Xiangfeng","family":"Wang","sequence":"additional","affiliation":[{"name":"Beijing Advanced Innovation Center for Food Nutrition and Human health, China Agricultural University, Beijing, China"}]},{"given":"Zhongfu","family":"Ni","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 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