PRS with Plink - troubleshooting
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8 months ago
dolphiness • 0

Hello!

I'm trying to compute PRS for different p-values and that's my code:

plink1.9 --bfile phe.gen.data --score summary.stats.gz 1 6 7 header --q-score-range pvalue.threshold snp.pvals
--extract ID.valid.snp --out PRS

I get the following error in the log: Error: Line 4 of --score file has fewer tokens than expected.

I can't detect any problems with summary.stats.gz what can be the cause?

Thank you!

PLINK PRS • 326 views
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Is it clear that plink accepts a gz-file for --score? No mention in the doc. Otherwise it might help to see the first few lines of the (decompressed) file.

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plink1.9 --bfile phe.gen.data --score summary.stats.gz 1 2 3 header --q-score-range pvalue.threshold snp.pvals --extract ID.valid.snp --out PRS

That's the abbreviated summary stats (decompressed):

CHROM:POS37     ALT     BETA
10:100000625    G       0.017931
10:100000645    C       0.0065591
10:100002464    C       0.16826
10:100003242    G       0.016455

bim file:

1       1:752566        0       752566  G       A
1       1:752721        0       752721  A       G
1       1:754503        0       754503  G       A
1       1:798959        0       798959  A       G

And again, the same error: Error: Line 3 of --score file has fewer tokens than expected.

The summary stats and bim have the same variants and format. There are no missing values. I have no clue what's wrong.

Thanks.

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* Update* You were correct. It worked when I used the decompressed file.

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