How to plot SNPS

[Krithika-Bhuvan]

Is it possible to plot single nulcletotide polymorphisms (SNPs) on a circos plot ?
A SNP has the same start and end position. For example,
1:207620289 (rs12081383)
1:207624395 (rs72644189)

[venyao]

Do you mean plotting every single SNP as a point? In this case, if your SNP number is not very large, you can plot every SNP as a point by assigning every SNP a y-axis position. The start and end coordinates of a SNP can be the same.

In most cases, you want to plot the density of SNPs in specified genomic regions. If so, you need to calculate the SNP density.