walaj
commented
2 years ago Hi Giuseppe -- the answer is yes and no. SvABA will detect complex junctions like the ones in the figure, panel A, on the README. These are where there is a templated insertion of some other sequence at the breakpoint, on the order of 10s to ~100 bp, depending on the read length. These are coded in the VCF as "TSI_L" (where the rearrangement is described as the "local" rearrangements, e.g. green to orange and orange to purple), or as "TSI_G", which describes the larger rearrangement (green to purple). They are both included because it depends what you're interested in.
The length limit above is because svaba describes breakpoints, not overall genomic structure. The length of being able to phase complex variants is limited by the read length. For this large scale genomic structure, you need a tool like jabba (https://github.com/mskilab/JaBbA), or very long read sequencing.
On Thu, May 12, 2022 at 4:23 AM Giuseppe1995 @.***> wrote:
Hi, mine is more of a question than a actual issue, but I know that SvABA can somehow detect complex variants, although is not clear to me how to find them (in a matched normal-tumor call). Is it defined somewhere in the VCF header? I looked it extensively but I cannot find an answer. Thank you so much for your time!
Giuseppe
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Giuseppe1995
Hi, mine is more of a question than an actual issue, but I know that SvABA can somehow detect complex variants, although is not clear to me how to find them (in a matched normal-tumor call). Is it defined somewhere in the VCF header? I looked it extensively but I cannot find an answer. Thank you so much for your time!
Giuseppe