It appears that the "type of connection" (the [p[t style notation) is mislabeled for many of the BNDs called. I have attached an excel file with an example for each of the 4 types of connections. I have also attached screenshots showing the reads spanning the breakpoints. Finally, I'm attaching drawings of the expected and actual type of connection (the second one I believe is correct, but the other three do not match). The "expected" is the type of connection that I expected based on the label from sniffles. The "actual" type of connection is what I am seeing from the reads spanning the breakpoints. I got the definitions for the types of connections from the documentation of VCF format here. Of note, their figure 2 images match my interpretation of the type of connection.
It appears that the "type of connection" (the [p[t style notation) is mislabeled for many of the BNDs called. I have attached an excel file with an example for each of the 4 types of connections. I have also attached screenshots showing the reads spanning the breakpoints. Finally, I'm attaching drawings of the expected and actual type of connection (the second one I believe is correct, but the other three do not match). The "expected" is the type of connection that I expected based on the label from sniffles. The "actual" type of connection is what I am seeing from the reads spanning the breakpoints. I got the definitions for the types of connections from the documentation of VCF format here. Of note, their figure 2 images match my interpretation of the type of connection.
bnd_examples.xlsx bnd_expected_actual.pdf
