Question: What are the strands of structural variant breakpoints?
gravatar for weishwu
2.4 years ago by
weishwu30 wrote:

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:

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 (, 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?


vcf sv • 1.1k views
ADD COMMENTlink modified 7 weeks ago by trausch1.5k • written 2.4 years ago by weishwu30

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!

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by renny0
gravatar for trausch
7 weeks ago by
trausch1.5k wrote:

I am not sure about other tools but delly outputs INFO/CT which captures the orientation of SV breakpoints. The mapping of SV breakpoints to potential fusion genes is explained here.

ADD COMMENTlink written 7 weeks ago by trausch1.5k

Dear trausch, Many thanks for you reply. Your reply reminded me that I may not be able to treat the SV input required by shatterseek as BEDPE format (in fact, I thought so, because the example attached with shatterseek is very similar to the bedpe format), but I still don’t know how to convert vcf accurately for the proper format, the shatterseek tutorial ( are very confusing. Do you have some suggestions.

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by a6618810
gravatar for a661881
7 weeks ago by
a6618810 wrote:

Dear weishwu, Happy to see this topic, I meet the samle problem recently. I am tried the tool called svtools noticed by renny, But I find the translocation SV seems incorrectly after convert. Could you please share me some information. Best. Zhang

ADD COMMENTlink written 7 weeks ago by a6618810
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