Table 2.
PRS Software
| Software/Program | Approach1 | Traits2 | OS (Language)3 | Website |
|---|---|---|---|---|
| PLINK | P+T (manual threshold) | B, C | L, W, M | https://www.cog-genomics.org/plink2 |
| PRSice-2 | P+T | B, C | L, W, M (R) | http://prsice.info |
| LDpred | Bayesian mixture, P&T | B, C | L, W, M | https://github.com/bvilhjal/ldpred |
| JAMPred | Bayesian mixture | B,C | L, W, M (R+Java) | https://github.com/pjnewcombe/R2BGLiMS |
| PRS-CS | Bayesian mixture | B, C | L (Python 2.x) | https://github.com/getian107/PRScs |
| SBayesR (GCTB) | Bayesian mixture | C | L, M | http://cnsgenomics.com/software/gctb |
| RSS | Bayesian mixture | C | L (MATLAB) | https://stephenslab.github.io/rss/index |
| SBLUP (GCTA) | Linear mixed-effects model | C | L, M | http://cnsgenomics.com/software/gcta/ |
| lassosum | Regularized regression | B, C | L, W, M (R) | https://github.com/tshmak/lassosum |
1
P+T, pruning and thresholding.
2
B, binary (case/control); C, continuous.
3
L, Linux; W, Windows; M, MacOS.Plink binary format is supported by all programs with the exception of RSS, which only requires the summary statistics file. Summary statistics input formatting varies but minimally requires effects estimates and their standard errors, p-values, and Ns. PRSice-2 can additionally take imputed data in Oxford .bgen v1.1/v1.2 format.