Large deletion filtered out about sniffles HOT 2 OPEN

Hello Sumudu
It looks like Sniffles is only using the reads marked in red for that call. Can you confirm it with the read names you have in the INFO field under RNAMES
It seems that the other reads were not used, likely based on position. We would like to investigate further that issue. Could you please run the sample again and adding the --no-qc flag and sharing the output SVs that are in that region. It could be only columns 1,2,3,7,8 and 10 from the VCF file

Best
Luis

from sniffles.

Hi Luis,

Many Thanks for your feedback.

As you said the RNAMES are the ones you marked in red. And I tried with the --no-qc option with sniffles 2.3.3 latest version. It detects the large (~12, 150bp) deletion. But VCF has more than one entry for the same deletion with different RNAMES. I attached here the extracted region of interest in a .txt file for your reference.
In this case, what would be the best way to run sniffles? Greatly appreciate your help to understand this.

I also have hybrid SVs in CYP2D6 gene that represent as insertion which I'm trying to figure out. I'll post it as a separate issue.

Thank you
Best
Sumudu
test.txt

from sniffles.