This question is to be read in the context of data protection. It seems to be common understanding that the whole genome sequence of an individual is personally identifiable, non-anonymizable information: if you possess the whole genome sequence, you can without any doubt identify an individual. You also cannot anonymize it, because you would need to obstruct the genome sequence in some way, making it useless for any diagnostics or research.
But how about Variant Calling files (specifically referring to the VCF file format)? You reference against a known genome, but you neglect structural changes such as translocations, duplications and deletions. Can you still identify a person based on a Variant Calling file?