Calculate PGS score from UKB data using PGS Catalog #3719
Unanswered
iris-garden
asked this question in
Support Requests
Replies: 1 comment
-
Note The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated. (Nov 09, 2023 at 19:02) danking said:Hey irun! If you’re just computing PRS scores for samples stored in BGEN with scores stored in compressed text, I don’t think Hail will provide much additional benefit. Hail shines when you use it for an entire analysis on data in Hail native format. Things like QC’ing a sequencing matrix, computing PCA, LD, and performing regressions. FWIW, we do have an example of how to use Hail to compute PGS. |
Beta Was this translation helpful? Give feedback.
0 replies
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
-
Note
The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.
(Nov 05, 2023 at 09:05) irun said:
Hi!
I am trying to calculate polygenic risk scores (PRS/PGS) for UK Biobank data (imputed bgen files) using pre-computed scores from the PGS Catalog available online.
So basically I’m just trying to code a script that takes as input a file with the pre-computed scores from PGS catalog, as for example, this file: https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000001/ScoringFiles/Harmonized/PGS000001_hmPOS_GRCh37.txt.gz ; and bgen files (one per chromosome) from UKB. Then the script will map the variants present in PGS Catalog with those present in UKB, and the beta values (coming from the PGS Catalog file) for each variant for each individual will be summed up to calculate the PGS per individual.
Here is a bgenix and plink version of what I am considering doing but using Hail instead: PRS Pipeline
Is there something similar already available?
Do you think it is sensible to use Hail for this use-case or should I keep with bgenix or plink? As I hope I explained, I am not trying to compute develop or validate PRS scores, but just do a “mapping of the variants” and use the scores already computed in the PGS Catalog.
Thank you in advance!
Beta Was this translation helpful? Give feedback.
All reactions