I have a variant call file from GATK. I want to Extract only sites that are polymorphic between samples and not necessarily between samples and the reference.
You might try using discordance in SelectVariants. https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php#--discordance
You can compare each sample against the other samples.