I have a vcf file that I have been processing and I have been tracking my SNP counts throughout the processing steps. However, upon removing several individuals from the dataset, the SNP count remained the same as before. Does anyone have any insight as to why this might have happened? For reference, the species being studied is a grass with three subspecies. The removal of these individuals was done to process out the two subspecies.
use 'bcftools view --samples ...'