Closed zhemingfan closed 1 year ago
Hi there, thanks for this bug report!
Do you have any indication that there may be a real variant here that's being incorrectly reported? (i.e. from looking at the region in IGV). If you have a sample BAM file subsetted to this region that you're able to share, I can also test on my end.
One possibility is that there is a foldback inversion over an area with an insertion. I would still consider it a bug, but it's a bit tricky to solve since it's related to how aligners report insertions in supplementary alignments (often they are not explicitly reported).
So for example you could have a case like this:
I've simplified a bit, but currently, there is nothing in SAVANA to account for cases like the above (where there are missing bases in the supplementary/softclipped regions). I will have to think further on how to address this.
Does this explanation seem like it fits to your example?
This seems to be resolved in the new version, closing this issue. Thank you!
Hi @helrick,
I was testing SAVANA, and noticed I got the following call in the strict VCF output. How do I interpret this results? Based on your previous comment this post, this should be a deletion-like signal, but is the intended behaviour to call a 1 bp deletion?
These are the parameters I used to run SAVANA: