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B allele frequency (BAF) simply refers to the fraction of reads supporting non-reference alleles at a given SNV position. This measure can be extracted from aligned alleles at each position with SNV call and helps to define CNV regions. For example, in one-copy deletions, one would expect to see decreased sequence count and general lack of clustering of B allele frequency around 0.5, compared to neighboring regions without deletions. As in the original algorithm, PennCNV-Seq also uses “2” for markers without information about allele frequency.
Copyright and License information: The Author(s) ©2017
Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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