Low number of SVs

[lubertorubior]

Hi, I have started using cue as I find it a very interesting approach.

As I want to evaluate its performance, I tested it with the HG002 sample (Illumina, ~35X, 2x150bp) aligned using BWA-MEM to hg19.

I ran it in docker with default parameters using the cue.v2.pt model and it finished without errors.

I got ~400 SVs in the resulting VCF file. Is this a low number for the whole genome or does it work as expected?

Thank you for your time
Best wishes!