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.
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.
