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. 2015 Feb 28;16(1):66. doi: 10.1186/s12859-015-0502-7

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© Qin et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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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Homologous sequence mediated SV simulation. The types of homologous sequence (e.g., transposable elements) medicated SV simulated by SCNVSIM are: A) TE-mediated deletion; B) TE-mediated tandem duplication; C) TE-mediated inversion (two TEs are on opposite strands); D) TE-mediated translocation (balanced or unbalanced); and E) TE-mediated insertion (intra- or inter-chromosome). Break points are randomly picked in homologous sequences shared by compatible repeat elements which are from the same repeat family and overlapping with each other.