Question: PLINK Error: No valid entries in --score file.
0
gravatar for Cindy
4 months ago by
Cindy20
Cindy20 wrote:

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
snp plink • 301 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 4 months ago by Cindy20
1

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

ADD REPLYlink modified 3 months ago by RamRS20k • written 4 months ago by chrchang5234.8k

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

ADD REPLYlink modified 3 months ago by RamRS20k • written 4 months ago by Cindy20

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

ADD REPLYlink modified 3 months ago by RamRS20k • written 3 months ago by chrchang5234.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1830 users visited in the last hour