VCF file from Manta annotated with VEP as input

[YussAb]

Hi to everybody and thanks for your work,

I'm using vcf2circos to generate circos plots from VCF files that were annotated with VEP.
In particular I would like to visualize informations about the STRAND (+/-) that will be very useful for my purpose.
I can get this information after annotating my VCFs with VEP, but I'm not able to display it.
Furthermore it's not yet clear to me if the package is specifically designed for VCF inputs annotated with AnnotSV in VCF mode, or if there is flexibility to integrate other annotators.

Thank you in advance!
best reagards,
Youssef

[JbaptisteLam]

Hi,
Sorry for late response,
First of all, in the configuration file (options.json) in dict["Variants"]["annotations"]["fields"] you can specify which info fields to display in the hover, if the fields is in the vcf info field, it will be display.
This tool was effectively developped to deal SV vcf especially comming from AnnotSV but you can have both SNV and InDels. But wherever your VCF comes from, vcf2circos could handle it.
Best,

Jean-Baptiste