How to prepare the data for Circos SNV, CNV and SV visulaization in one plot

[Neha Goel]

The image is a Circos plot, which provides a visual representation of genomic mutations within a genome. This type of circular visualization is commonly used in genomics to show structural variations, single nucleotide variants, and copy number alterations.

Image should be 

1. Outer Ring (Chromosomes)

   • The outermost ring represents the chromosomes of the genome.
   • Each chromosome is labeled numerically (1–22, X, Y) and color-coded.

2. Inner Rings (Mutation Annotations)

   • Various types of mutations and structural variations are represented in different formats.

3. Types of Mutations Represented:

   • Point Mutation (SNVs - Scatter plot, small dots), Indels

     • Represented as small dots (likely red) on different chromosomes.
     • These indicate specific nucleotide changes.

   • Copy Number Changes  as Heatmap or stacked histogram

     • Shown as a continuous track inside the chromosome ring.
     • Different intensities of shading likely indicate copy number gains or losses.

   • Intrachromosomal Rearrangements SV (Inversion, deletions)

     • Lines connecting two regions within the same chromosome.
     • These indicate structural changes such as inversions or duplications.

   • Interchromosomal Rearrangements Tranlocations

     • Lines linking different chromosomes.
     • These represent large structural variants such as translocations, where a segment of one chromosome moves to another.