Computing multiple PRS on the fly with plink
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5 weeks ago
WD • 0

Hello,

I have the following type of file

ID     var  Beta_1 Beta_2 Beta_3 .... Beta_100
rs1     A    -0.6       0.0   0.3 ...    0.2
rs2     G     0.4       0.2   0.0 ...   -0.7
...


I would like to use the --score function of plink to compute PRS for each column.

My main problem is that I can run plink column by column with something like plink --vcf chr1.vcf.gz --score score.txt 1 2 3

But that requires loading each chromosome per column Beta_k which takes a lot of time. Is there a simple way to parse the different columns and to compute the prs for each column?

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Are all rsids in chr1?

0
Entering edit mode
5 weeks ago

plink 2.0 has a --score-col-nums flag that lets you compute multiple scores at a time.