PLINK Error: No valid entries in --score file.

Question

[Cindy]

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

Answer 1

[chrchang523]

Check whether any variant IDs and alleles in your --score file exactly match the ones in all.bim.

[Cindy]

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

[chrchang523]

Use plink 1.9's --gen flag to read your .gen file directly (and --sample to read the .sample).