Plink error with reading phenotype file

Question

[MAPK]

Hi All,

I am having issues with plink as it is not able to detect pheno file( $METADATA as shown below) and I was wondering if someone has solution. Thanks!

[AN@AN 03-PLINK-QC-files]$ head $METADATA
FID     IID     SEX     STATUS  WXS
10R_R48 10R_R48_11      2       2       2
10R_R48 10R_R48_1       2       2       1
10R_R54 10R_R54_10      2       1       2

This is the command I am trying to run:

plink1.9 --bfile ${BFILE} --pheno ${METADATA} --pheno-name WXS --test-missing --allow-no-sex --out ${BFILE}-missing-WXS

This is the log I am getting which says 0 phenotype values present after --pheno. which obviously means it's not reading my phenotype file. Is there anything I am missing here?

PLINK v1.90b6.4 64-bit (7 Aug 2018)            www.cog-genomics.org/plink/1.9/
(C) 2005-2018 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to FASe_3894_WXS_SNPS_INDELS-hwe-geno0.05-mind0.1-missing-WXS.log.
Options in effect:
  --allow-no-sex
  --bfile FASe_3894_WXS_SNPS_INDELS-hwe-geno0.05-mind0.1
  --memory 100000
  --out FASe_3894_WXS_SNPS_INDELS-hwe-geno0.05-mind0.1-missing-WXS
  --pheno Final_Pheno_FASe_3894.txt
  --pheno-name WXS
  --test-missing
  --threads 12

773748 MB RAM detected; reserving 100000 MB for main workspace.
2901689 variants loaded from .bim file.
3892 people (0 males, 0 females, 3892 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
FASe_3894_WXS_SNPS_INDELS-hwe-geno0.05-mind0.1-missing-WXS.nosex .
0 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 3892 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.996216.
2901689 variants and 3892 people pass filters and QC.
Note: No phenotypes present.
Warning: Skipping --test-missing since at least one case and one control is
required.

Answer 1

[chrchang523]

Check the correspondence between FID/IID in $METADATA and FID/IIDs in your .fam file.

[MAPK]

Hi, Thanks for your comment. I think that makes sense. How do I add actual FID in my BFILE? Right now, I have IID and FID same in .fam.

This is the command I used to create BFILE. How do I add actual FID instead of --double-id?

plink1.9 --vcf ${VCF} --double-id --keep-allele-order --make-bed --out ${BFILE}