VCFTools Removing Individuals and SNP counting

Question

[adnichols]

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.

[Pierre Lindenbaum]

use 'bcftools view --samples ...'

Answer 1

[inedraylig]

Generally, vcftools will not remove any SNPs, but will set the GT score to missing (./.) for the individuals you remove. I second Pierre's recommendation to prefer bcftools, where the use is far more clear on what the filtering steps do.