Does lumpy filter out multiple alleles？

[hhd1008611]

Dear teacher,

I hope this message finds you well. I am currently working on structural variation (SV) genotyping using Lumpy and encountered a question I was hoping you could help clarify.

By constructing a fitting curve, I found that the p-value for a multi-copy repeat is 10^-9. However, when analyzing the SV genotyping data generated using Lumpy, the mixed linear model shows no significant SV in this region. I am wondering if Lumpy could be filtering out multi-allelic variants in this case.

Your insights or suggestions would be greatly appreciated.

Thank you in advance for your time and assistance.