ASK: How can I filter controversal imputed result?

[duaghk]

Hello,

I am currently using GLIMPSE2 for rare variant detection and came across a confusing result.

In the attached image, you can see that there are multiple imputed results (3 rows) for the same genomic position (chr1:10397). Each result appears to differ in the REF and ALT alleles, while the genotype calls for all three are 0|0.

Here are my questions:

How should I interpret these results? Why are there multiple imputation outcomes for the same position?
How should I filter or prioritize these results? For downstream analysis, which entry should I use or trust in this case?
If you have any suggestions on how to handle or clean such data, I’d greatly appreciate it.

I used GLIMPSE v2.0.0, and input vcf was generated by: LP-WGS -> DeepVariant call -> Filter PASS & DP >=5

Thank you in advance!