Unclear CT field

[SergioManzano10]

Hi everyone,

I am having trouble interpreting the CT (Connection Type) field in VCF files, particularly in the following cases:

1. When SVTYPE=BND, and the CT field is set to 5to3, I interpret this as the event occurring between strands (+, -).

2. When SVTYPE=DEL, and the CT field is also 5to3, I again interpret this as the event occurring between strands (+, -). However, since deletions occur within the same chromosome, interpreting 5to3 as the sense strand (+) would be inconsistent with the expected DNB interpretation (I would be interpreting the CT as the direction of one single strand).

How can I resolve this discrepancy?