typed only sitets about imputationserver HOT 1 OPEN

I have the same question:

Which part of the TOPMed process excludes the variants that appear in the typed-only.txt file?

The quality control statistics from in the TOPMed server state: Reference Overlap: 79.50 %

And the typed-only.txt file contains 20.50% of the genotyped variants. So it looks like these variants are excluded because the do not overlap with the reference. However, all of these variants match by chromosome-position-ref-alt to the TOPMed variants downloaded from the bravo server.

The TOPMed documentation includes the following sentence under Phasing:

Please note: Target-only sites for unphased data are not included in the final output.

Could it be that the variants in the typed-only.txt file are excluded during phasing?
If so, I do not understand why the aforementioned 20.50% of my genotyped variants would be target-only, since they exists in the TOPMed panel.

Also note that about ~80% of the excluded variants are subsequently imputed by TOPMed, i.e. they are included as imputed variants in the TOPMed results.

from imputationserver.