VCF to Circos format(s)

[bzdyelnik]

Hi,

Does anyone know if there is a utility out there (vcfutils.pl from samtools? vcftools?) that can convert variants in a VCF file to a file that can be loaded into Circos for visualization? (e.g. highlights track)

Or has everybody just rolled their own and kept it private?

Thanks,

Jesse

[sdvie]

It would be definitely interesting to have a good
= interactive+graphical+platform-independent
visualizer for vcf files (also customized ones with extra fields).

[apadr007]

Has anyone fold a solution to vcf files and circos?

[gaffa]

Unless you want to do something really sophisticated it's often easy to parse things out with simple unix one-liners (cut, grep, awk etc.) and format them into the Circos formats.

[id0]

This thread is now two years old, but still seems to be the most relevant hit on the subject. Is there still not a proper VCF to CIRCOS tool?

[ambu]

Apparently this thread is 10 years old now, yet no clear answer.