How to draw circular plot to show genomewide snps and indels distribution?
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4.7 years ago
mirza ▴ 150

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

circular plot snp distribution • 1.9k views
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The paper you linked includes a citation for circos which was used to generate that figure.

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

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

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4.7 years ago
Titus ▴ 910

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