I am trying to convert my merged vcf file of 500 samples to text file formats (.ped and .map) using
plink --vcf $vcf --allow-extra-chr --pheno Phenotype_LA_as_vcf_order.txt --all-pheno --update-sex Phenotype_LA_as_vcf_order.txt 3 --keep-allele-order --recode --out snp-LA-Association command. Unfortunately, it keeps giving me an error saying
Error: Invalid sex value on line 2 of --update-sex file. (Acceptable values: 1/M = male, 2/F = female, 0 = missing.), even though the tab dilimited file I used for
--update-sex is filled with the acceptable values of "1" and "2" to indicate "male" and "female" respectively on the third column.
Does anyone know a way to fix such an error? Any suggestions will be of great help. Thanks.