PLINK Error: No valid entries in --score file

Question

[V.Zanin]

Hi,

I ran this command on plink1.9 to calculate the poligenic score.

plink --vcf sample --score output.txt 1 2 3 --out poligenic_results

- output.txt: 
ID      ALT     UKB-b-15541
rs10399793      C       0.000345793
rs2462492       T       -0.00027716

- sample.vcf:
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  K02A000008_K02A000008   0_HG00096       0_HG00097       0_HG00099       0_HG00100  >1       10177   rs367896724     A       AC      .       .       PR      GT      ./.     0/1     0/1     0/1     0/1     0/0     0/1     0/1     0/1     0/1>

PLINK v1.90b6.21 64-bit (19 Oct 2020)          www.cog-genomics.org/plink/1.9/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to poligenic_results.log.
Options in effect:
  --out poligenic_results
  --score output.txt 1 2 3
  --vcf sample.vcf

241818 MB RAM detected; reserving 120909 MB for main workspace.
--vcf: poligenic_results-temporary.bed +
poligenic_results-temporary.bim + poligenic_results-temporary.fam
written.
4582 variants loaded from .bim file.
504 people (0 males, 0 females, 504 ambiguous) loaded from .fam.
Ambiguous sex IDs written to poligenic_results.nosex .
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 504 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.00198413.
4582 variants and 504 people pass filters and QC.
Note: No phenotypes present.
Error: No valid entries in --score file

I've also tried to transform the --vcf file into a plink format file .bim .fam .bed with the following command

plink --bfile sample --score output.txt 1 2 3 --out poligenic_results

Does anyone have any hints?

[chrchang523]

Did you verify that there were overlapping variants between sample.vcf and output.txt?

4582 is an awfully small number of variants for a VCF file, so there may simply be no overlap. Alternatively, the variant IDs may be formatted differently between the two files.

Answer 1

[bk11]

You can delete the header of your output.txt file and then run plink --score function.

#deleting the header from `output.txt` file
sed -i -e '1d' output.txt

#generating score where score reads variant IDs from column 1, allele codes from column 2, and scores from column 3 of your output.txt file
plink --vcf sample --score output.txt 1 2 3 --out poligenic_results