Definition of oriantation region of breakpoints

[infotmatician]

Hi, Thank you for developed such a great tool. How can I specify variant direction using VISOR according to VCF4.2? I am a little bit confusued about HACk, when want to generate translocations. I am trying to do bechmark of SV tools for long reads. As an example, 1 10000 30000 reciprocal translocation h1:20:420000:forward:reverse 0 Does this variant should align the left of 20:420000 or right of 20:420000? Best regards

[davidebolo1993]

Hey @infotmatician,

the example line you provide basically substitutes 1:10000-30000 with 20:420000-440000 (length here is 20000) and viceversa. That's what a reciprocal translocation is supposed to do. A simple script to convert HACk .bed to .vcf is referenced in this issue here: this does not cover every possible cases but should be a good starting point.

Let me know if this helps,

Davide