How to draw circular plot to show genomewide snps and indels distribution?

Question

[mirza]

Hi,

I have 2 related fungal isolates and am working on variant calling. I have called variants using samtools-bcftools and have annotated them using snpEff. What tools can I use to draw a circular plot to represent snps and indels distribution?

I want to generate a plot like this Genome analysis of rice-blast fungus Magnaporthe oryzae field isolates, Figure 3

Here is the link to the paper https://doi.org/10.1016/j.gdata.2015.06.018

[GenoMax]

The paper you linked includes a citation for circos which was used to generate that figure.

[Joe]

Another option is BRIG (though the resolution of the image on large genomes can make snps etc hard to see)

[VHahaut]

If you want to do it in R, I found circlize quite useful and easy to understand. circlize Cran

[mirza]

thank you all for your reply.

Answer 1

[Titus]

Hi , Looks like you are looking for some circos plot , there is this discussion on biostars which can interest you : Circos-How To Generate Circos Image Of Snp And Indel Across Chromosomes