Apply VCF to reference

[Mossy-Frog]

Hello !
Love what you did with cuteSV, thank you for your work.
I struggle to transform the output VCF in any format that would enable me to apply the structural variants to the reference genome, thus creating the "proper" sequence. Do you know if there is any way to do it ? I tried bcftools and GATK, but none recognises correctly the VCF...

[CoREse]

Hi, Mossey-Frog,

My suggestion is that you can try VISOR to apply variants into a fasta file. To do that, you should transform VCFs into BEDs that VISOR needs, I believe there are several tools that can do that, or you can do it by writting your own script, it's not very complicated.

Best wishes,
CRE