If the VCF is too large to upload, users can upload a VCF file for only a single chromosome, a subset of samples, or a specific set of SNPs for the chosen model.
# extract a specific chromosome
for chr in {1..30};
do
vcftools --gzvcf NameOfVCF --chr chr$chr --recode --recode-INFO-all --out chr$chr
done
# extract specific positions
vcftools --gzvcf NameOfVCF --positions specific_position.txt --recode --recode-INFO-all --out specific_position
# keep subset of samples
vcftools --gzvcf NameOfVCF --keep id.txt --recode-INFO-all --recode --out subset
