Hi,

This is kinda dumb question but I haven't got a clear yes/no answer. Just needed to be sure what I did is right.

Let's say I have a binary file from a vcf (#1). Then, either I want to update the FID/IID columns or add the phenotype (#2) on the binary file.

1: plink --vcf --keep-allele-order in.vcf --make-bed --out binary --allow-no-sex 2: plink --bfile binary --update-ids ID.text --make-bed --out binary2 --allow-no-sex

Questions

• Should I follow the same order of the samples listed in the binary file when updating IDs? I thought Plink1.9 looks for sample names matched and changes it, is it the case? so everything related to that sample (maf, SNPs called, etc) is changed accordingly?
• When updating the FID/IID or Phenotype on binaries, does Plink1.9 impose the order you state in the ID.txt ?

Thanks