How to imputate chrX using GLIMPSE2

[raksasa]

Hi,
I am trying to imputate chrX using GLIMPSE2, but not like GLIMPSE1, I found that there is no tutorial for chrX. I think the GLIMPSE1 workflow process chrX different to autosomal when preparing referenc panel (when calculating GL, the ploidy is setup by bcftools), while GLIMPSE2 do not document such step, and no ploidy parameters found in GLMPSE2_phase. Then what should I do if i am using BAM as input? or something I have misunderstoold?

thanks in advance~

[salim0mans]

Hi,
The authors indeed have a tutorial for Glimpse chrX imputation, but it's in Glimpse1 site:
https://odelaneau.github.io/GLIMPSE/glimpse1/tutorial_chrX.html
I believe the commands and flags are basically the same for Glimpse2.
The ploidy-related flag is --samples-file