PGS weights for comparative evaluation of polygenic scoring methods in five biobanks

These files contain polygenic (risk) score (PGS/PRS) weights from 7 methods produced with prspipe (https://github.com/intervene-EU-H2020/prspipe). Variant positions and reference alleles can be found in the prspipe repository (HapMap3-1KG variants). A subset of these scores were evaluated in Monti et al. [1], and will be made available on the PGS catalog (https://www.pgscatalog.org/), which presents the preferred way to access those scores.Scores are based on GWAS summary statistics hosted on the NHGRI-EBI GWAS Catalog (https://www.ebi.ac.uk/gwas/home) under CC0 license unless stated there otherwise. When using these scores, please cite the study/studies which provided the summary statistics (identifiers starting with <i>GCST</i>), as well as the manuscript [1] and tool used to create the score.[1]<br><br>The scores for p-value thresholding followed and clumping (pt_clump) provided here are not nested. To make these scoring files nested, the following command can be used:<br><br>zcat INFILE | awk '{ if(NR==1){for(i=3; i&lt;=NF; i++){$i=$i"_nested"}; print $0} else{for(i=3; i&lt;=NF; i++){ if(c){$i = c}; if($i != 0){c = $i}}; print $0; c=0}}' | gzip &gt; OUTFILE<br><br>where INFILE should be the path to the input file (e.g. prs/pt_clump/GCST008059/1KGPhase3.w_hm3.GCST008059.score.gz) and OUTFILE is the the path to the output file.<br>