Genotyping SVs from Different Callers

[Lukecassar21]

Good Afternoon,

I'm writing this to see if BayesTyper would be the ideal genotyping tool for my use case.

I am currently calling structural variants from 1000~ samples using Manta, Smoove, CNVkit, and CNVpytor/CNVnator (potentially MELT as well). I am merging these variants together usng a program called JasmineSV with very positive results (maintains the format of the variants from their original caller VCFs). The only issue is that I'm not certain on how to incorporate BayesTyper into my workflow due to this process. It's very important to re-genotype all of my structural variants.

In addition to this, is BayesTyper capable of genotyping all of the following?:

1. Deletions
2. Insertions
3. Dispersed Duplications
4. Mobile Element Insertions
5. Breakends (Translocations and or Inversions)
6. Inversions
7. Tandem Duplications

I am aware that some of these are quite obvious but I just want to confirm that all of them can be genotyped using BayesTyper. If for some reason I cannot or should not use BayesTyper for my situation, do you have any recommendations?

I'm still relatively new to structural variant calling and genotyping but I would greatly appreciate any clarification and insight into the matter.