How to format plink2 pheno file?
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4.9 years ago
anamaria ▴ 220

Hello,

I was running this command:

plink2 --threads 40 --vcf VCFchr22.vcf.gz  --pheno pheno_Mtt.txt --pheno-name pheno --glm --out FINchr22

where my pheno_Mtt.txt looks like this (space separated):

      FID     IID pheno
1 1000017 1000017    -9
2 1000025 1000025    -9
3 1000038 1000038     1
4 1000042 1000042    -9
5 1000056 1000056    -9
6 1000074 1000074    -9

but I am getting: No entries in pheno_Mtt.txt correspond to loaded sample IDs.

The same error I get if I just have IID and pheno column tab separated in my pheno_Mtt.txt file.

Please advise, Thanks Ana

plink2 • 1.9k views
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