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Fig. 2 | BMC Bioinformatics

Fig. 2

From: cnvCurator: an interactive visualization and editing tool for somatic copy number variations

Fig. 2

An example of missed CNV call. The shown region in the main window is base pairs 105017997-139523334 on chromosome 4. The two vertical lines (purple on the left, and blue on the right) in the main window delimit the boundary of a segment of copy number neutral (Chr4: 108239101-136127300) called by CONSERTING, with the breakpoint alignments displayed in the two separate pop-up windows. Upon manual review we found this segment contain a sub-segment of copy number loss (marked in rectangle with dashed blue line), as supported by three lines of evidences: 1) decreasing read depth in tumor over normal, as shown in the tracks of read depth and the track of logR ratio of tumor to normal; 2) the corresponding change of BAF pattern as shown in the BAF track; 3) the breakpoints of this sub-segment are in the exact position separating the soft-clipped part from the matched part of multiple split reads in the tumor bam, but not in the normal bam (shown in Fig. 3)

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