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. 2019 Mar 20;9:119. doi: 10.3389/fonc.2019.00119

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Copyright © 2019 Halperin, Liang, Kulkarni, Tassone, Adkins, Enriquez, Tran, Hank, Newell, Kodira, Korn, Berens, Kim and Byron.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Example lumosVar 2.0 output. (A) Log2 fold change of the mean exon read depths compared to the unmatched controls. (B) The estimated integer copy number states are plotted for each genomic segment by chromosome position. (C) The variant allele fractions are plotted by chromosome position. The gray and brown dots represent variants called as germline heterozygous by lumosVar 2.0 and the large colored dots represent variants called somatic by lumosVar 2.0. (D) Summary of the clonal variant group patterns. The thickness of the lines represents the proportion of copy number events assigned to each group and the size of each circle is proportional to the number mutations assigned to each group. (E) Sample fraction (estimated proportion of cells in the sample containing the variant) distribution of somatic mutations. (F) Number of exons determined to be in each copy number state, excluding diploid. (G) Number of somatic mutations detected in both samples (left bar), enhancing only (middle bar), and non-enhancing only (right bar). On all plots, the colors indicate the clonal variant group.