Searching for substitutions in a VCF file

[Rubal7]

Hello all,

I've used GATK to produce snp and indel calls for genomes of multiple individuals from multiple populations. I want to identify the sites where there are substitutions between the populations. I have done this with snp array data but am unsure how this is best done with VCF files.
Can anybody recommend a good way to do this? I have not yet found a way to search for substitutions or to specify comparing certain groups of individuals within a vcf file (I have individual and population labels in the BAM files, not sure if this carries over to vcf format).

Thanks in advance for any help,

rubal7