Some questions

[svedziok]

Hello,
resulting vfc file from SV calling has column REF completely N and ALT columns contains N for translocations e.g N[21:10775188[

Do you know a reason for such result?

Best

[J35P312]

Hello there!
TIDDIT does not check which base is located at the start and end position of the SVs (mostly to save time; but also since no one have asked me to put the right base there yet!).

Hence the N only means that any base could be located at those positions; the N are only added for the sake of adhering the vcf format.

Maybe in the future I will make TIDDIT output the correct base instead, but it would require looking up those bases for each call.

Regards, and good luck!
Jesper