COVERAGE model missing for DEL causing AGGREGATED model to fail

[Lee-06]

Hello Dr. Eggertsson,

First of all thank you for this very useful software.

As I was looking for a way to have each structural variant mentioned only once in my vcf file I saw that I should use the aggregated model. However after further inspection of my results, I have noticed that out of my 174 scaffolds, 99% of the deletions that had FILTER=PASS were in the first scaffold (my longest one). The deletions in all the other scaffolds had no coverage model (only breakpoint) thus the aggregated model always had FILTER=LowPRatio.

I have tried changing the order of my scaffolds and doing the analysis without the first scaffold but the issue was not resolved, the coverage model would still appear only in that specific scaffold or just not be present at all for deletions. Any idea what that would mean ?

Best regards. Lee

[YiBenqiu]

Hi, I also have the same problem as you. Did you finally solve it?

[jingydz]

I am also concerned about this issue.