Detection of Reciprocal BNDs

[Carly-KT]

Hi,

Could you please explain how Sniffles detects reciprocal BNDs? Specifically, I really need to know why Sniffles detects a BND between chromosome 1:665050 (POS) and chromosome 3:2778480 (ALT) in the VCF output, but does not detect the reciprocal BND between chromosome 3:2778480 (POS) and chromosome 1:665050 (ALT) using the same reads? (There are no other detections close to chromosome 3:2778480 (POS).)

Read Details:

Read 1: d4ed0766-35dc-4e68-bf8f-d2283f2a20e8
• Read Length: 10,416 bp
• Primary Alignment: Chromosome 3 from 2,778,481 to 2,787,534 (MAPQ 60)
• Supplementary Alignment: Chromosome 1 from 663,636 to 665,050 (MAPQ 60)

Read 2: 56450bb9-7440-4d0a-a46e-a8727e20eb6d
• Read Length: 10,468 bp
• Primary Alignment: Chromosome 3 from 2,778,491 to 2,787,534 (MAPQ 59)
• Supplementary Alignment: Chromosome 1 from 663,635 to 665,049 (MAPQ 54)

Despite both reads supporting the BND from chromosome 1 to chromosome 3, the reciprocal BND from chromosome 3 to chromosome 1 is not detected.

Thank you!