structural variant vcf file comparison

Question

[tarek.mohamed]

Hi,

I have six vcf files (cases vs control) that contain structural variants with variable length from nanopore sequence run. These vcf files were generated using NGMLR aligner followed by sniffle.

What is the best way/tool to compare these files?

Thanks Tarek

Answer 1

[WouterDeCoster]

You can merge these SV vcf files using SURVIVOR, in which you can specify a distance to allow some variability between breakpoints.