Hi everyone,
I am having trouble interpreting the CT (Connection Type) field in VCF files, particularly in the following cases:
-
When SVTYPE=BND, and the CT field is set to 5to3, I interpret this as the event occurring between strands (+, -).
-
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?
Hi everyone,
I am having trouble interpreting the CT (Connection Type) field in VCF files, particularly in the following cases:
When
SVTYPE=BND, and the CT field is set to5to3, I interpret this as the event occurring between strands (+, -).When
SVTYPE=DEL, and the CT field is also5to3,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?