I'm trying to use a tool named ShatterSeek to call chromothripsis regions from SV calls. It requires me to list the breakpoint strands for each SV as input. For example, a deletion will be listed as:
11 8540385 11 8541773 DEL + -
A duplication is listed as:
14 61896354 14 62061596 DUP - +
As for INV, there are two types: head-to-head (5to5, or h2h) and tail-to-tail (3to3, or t2t):
2 36771088 2 75366617 h2hINV + +
17 35895909 17 36309972 t2tINV - -
The breakpoint strands are "+ -" for all DEL, "- +" for all DUP, "+ +" for all 5to5 INV, and "- -" for all 3to3 INV, as described here: https://github.com/GooglingTheCancerGenome/sv-report/wiki/VCF-output-formats
However I can't find any documentation about how to assign the strands for translocations which can have all possible strand combinations. As described in the VCF format documentation (https://samtools.github.io/hts-specs/VCFv4.2.pdf), the connection orientations of a translocation SV are denoted as:
REF ALT Meaning
s t[p[ piece extending to the right of p is joined after t
s t]p] reverse comp piece extending left of p is joined after t
s ]p]t piece extending to the left of p is joined before t
s [p[t reverse comp piece extending right of p is joined before t
Does anyone know what the strand combinations are for each of these four types of translocations?
Thanks.
Have you been able to find an answer on this? I was wondering the same thing. I was following the logic from svtools in how they assign internal strandness together with vcf specs and thought this: t[p[ + - t]p] + + ]p]t - + [p[t - - Deletion + - (provided in Shatterseek docs) Tandem dup - + (provided) Insertion + - (unsure?) This is assuming the breakend in the 5' region is + (head) and 3' region is - (tail). It would be ideal to confirm this before using the tool though. Any help would be greatly appreciated, thank you in advance!