Impact of custom hg38 with common alleles

[ekinda]

Hello, I am curious about the impact of using a custom reference genome with the most common alleles at each position edited in. As far as I could see, this is not mentioned in the original preprint.

1. Do you see an improvement in performance by using this approach?
2. How many positions are changed compared to hg38?
3. Did you try other approaches such as dynamically augmenting the data with the most common alleles, instead of a new reference?

Best
Ekin