zero variant matched during pgsc_calc

[ijlalhy...@gmail.com]

Hi,

Sorry for bothering you. I am working with ancient genome imputed data. Which I downloaded from https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/7RVV9N.

I wanted to perform PGS analysis using pgsc_calc. But I am running into an error 

matchresults = MatchResults(

                    ^^^^^^^^^^^^^
   File "/app/packages/pgscatalog.match/src/pgscatalog/match/lib/matchresult.py", line 184, in __init__
     raise ZeroMatchesError("No match candidates found for any scoring files")

I have checked the pfile, with the ref fasta using plink2 --pfile v66-ancient_eur-qced --ref-from-fa force --fa hs37d5.fa --make-pgen --out ancientEUR_normalized there were no problematic variants. I compared some variants manually with the scoring file; the positions are ok, but the effect and ref allele are swapped between the .pvar and the score file. Since I am working with an ancient genome and also performing PGS for the first time, I am not sure how to approach this problem. Is it the problem with the data, or am I doing something wrong?

I would really appreciate it if you could guide me in this regard.

Kind Regards,

Haider

[ijlalhy...@gmail.com]

In the meantime, I was able to solve this issue.