How to draw circular plot to show genomewide snps and indels distribution?
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
1 answer
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
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The paper you linked includes a citation for
circoswhich was used to generate that figure.Another option is BRIG (though the resolution of the image on large genomes can make snps etc hard to see)
thank you all for your reply.
If you want to do it in R, I found
circlizequite useful and easy to understand. circlize Cran