I have checked and found the problem. I used Gtool to convert .gen to .ped and .map which coded genotype as 11, 12, 22, and 00, while riskProfile uses T/C/G/A as named Allele. Is there any way to recode allele to AA, AB, BB and NN in my plink data? I only saw it can do reverse. Thanks
PLINK Error: No valid entries in --score file.
Hi all,
When I use plink to run --score function I got an Error:
No valid entries in --score file.
logfile:
PLINK v1.90b5.3 64-bit (21 Feb 2018)
Options in effect:
--bfile all
--out PRS
--score riskProfile.txt
Random number seed: 1543012864
32199 MB RAM detected; reserving 16099 MB for main workspace.
Allocated 906 MB successfully, after larger attempt(s) failed.
274205 variants loaded from .bim file.
7959 people (6370 males, 1589 females) loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 7959 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.970417.
274205 variants and 7959 people pass filters and QC.
Note: No phenotypes present.
Error: No valid entries in --score file.
I have checked the format of score file, it's like the following, and works before. I don't know what's wrong with the code, please help, Thanks
rs182786950 C -0.666783
rs3020682 G 0.127013
rs2379073 T 0.138857
rs10904559 T 0.0916695
rs34166011 G 0.213143
1 answer
Check whether any variant IDs and alleles in your --score file exactly match the ones in all.bim.
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chrchang523
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chrchang523
Use plink 1.9's --gen flag to read your .gen file directly (and --sample to read the .sample).
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Ram
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chrchang523
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chrchang523
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