Working example for VCF visualization in Circos

Question

[Charles Yin]

I would like to plot the SNP density of a genome plotted as histogram using Circos (http://circos.ca/), the inputs are a SNP variant calling VCF file and reference genome Genbank fasta file or Gbk file, I try to look for an example parameter for this plotting, but could not find exact solution. Would you please share with me if you have a working sample? Thank you!

[ibseq12]

hi genebow any more thoughts? did you manage to use circos for snp?

Answer 1

[Charles Yin]

I close this problem as I see the solution from Circos tutorial. The VCF file needs to be parsed as histogram file and the Circos uses this file for plotting.

The turorial is at here

Cheers!

[WouterDeCoster]

Thanks for sharing the solution, but there is no need to close the thread.