Combining chromosomes from .bed files about paper-ldpred2 HOT 2 CLOSED

There are many ways you can do that:

• combine the bed files with PLINK (I think I talk about that in another issue here).
• compute 22 predictions (one for each chr) and sum them.
• you can also maybe directly compute the scores from bed files using PLINK (maybe using all 22 chromosomes at once with first point) or using bigsnpr::bed_prodVec() and combining all 22 scores.

from paper-ldpred2.

Thanks for the options! I had already tried the PLINK option but I was having trouble merging the files because the variant names seem to have fallen away after I used vcftools to extract my list of SNPs. I was trying to avoid the second option but I know that one will work. Thanks again.

from paper-ldpred2.