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Fig. 1 | BMC Bioinformatics

Fig. 1

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

Fig. 1

An example of CNV call supported by multiple evidences. The interface of cnvCurator shows segment index on the left and various data tracks on the right. From top to bottom, the tracks include tumor read depth (red line), normal read depth (green line), logR ratio of tumor to normal (red for positive and blue for negative values, respectively), BAF (red dot), read alignment for tumor (in red box), read alignment for normal (in green box), and transcript annotation (blue). The shown region in the main window is base pairs 34766517–36142701 on chromosome 5. The two vertical shading lines (purple on the left, and blue on the right) in the main window delimit the boundary of the called CNV segment (Chr5: 34925308-35983911), with the breakpoint alignments displayed in the two separate pop-up windows. Within each pop-up window, the vertical black line delimitates the exact position of the breakpoint, and the red box and the green box display the tumor bam and the norm bam, separately. For the read displaying, split reads are in yellow–gray with the soft-clipped part in yellow and the matching portion in gray, and the others are discordant read pairs (purple - mate unmapped; red – mate in different chromosome; blue – mate in different strand; orange – mate in discordant distance)

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