Hi all,
I am working on PRS analysis these days and have some feature requests regarding SNP matching of the target data and GWAS summary statistics.

Allele frequency harmonization: When matching SNPs, I want to harmonize the allele frequency between two datasets so that I can validate transferability of PRS across different ancestries. Chisquared test looks suitable for finding outlier SNPs, supported by the fact that many of phasing detects potential mismatches between the target data and the reference panel with Xsquared statistics. But the thing is chisquared test in hail, ‘hl.chi_squared_test’, only takes integer value as input and gives pvalue and odds ratio as output. If I’m going to run a chisquared test with allele frequency and want to get a chisquared value, what should I do? Do you guys have any plan to implement this in the function?

SNP matching: One of the most popular PRS methods, Bigsnpr (R) matches SNPs from two different datasets by chromosome and position with 3 steps below. I wonder whether you guys are willing to construct this kind of SNP matching function.
 Remove ambiguous alleles [A,T], [T,A], [C,G], [G,C]
 Match SNPs , flipping the strand (ex. A ~ T)
 Match SNPs, reversing the allele (ex. alleles[0] == A1 & alleles[1] == A2)
Also, minor issues. Do you guys have any plan to incorporate PRS computation algorithm (PRScs, for example) other than plink sum? And would it be possible for ‘hl.sample_qc’ to support het_freq_hwe metrics like ‘hl.variant_qc’ function by any chance? I want to replicate the preimputation QC conducted by ricopili thus need Fhet value. (RICOPILI  Preimputation (QC))
Hope to hear from you soon.
Thanks!