I am trying to extract fixed sites within the sample from a VCF file. By fixed sites, I mean those that differ from the reference genome but that are fixed within the sample.
REF ALT ind_1 ind_2 ind_3 1 A C 1/1 1/1 1/1 2 G T 1/1 0/1 0/0 3 C G 1/1 1/1 1/0 4 G C 0/1 1/1 1/0 5 A G 1/1 1/1 1/1
For instance, this is was a simplified version of a VCF file. In this case, sites 1 and 5 belong to this category of sites that contribute to divergence. Is there any tool on vcftools or R package that I can use for this purpose?
Thanks in advance.