Your question really lacks a lot of details, you should explain in more detail what kind of data you have and what you want to accomplish.

Anyway, for getting SNPs, see the "Finding SNPs in a Sequence Using BLAST" tutorial and blast_snp_extractor.pl.

I don't think BLAST is the proper tool to deal with copy number variation, but you could parse its output to get queries with multiple hits on the same subject sequence, with overlapping coordinates (on the query) and similar e-values. Of course, this is very crude and you should blast against whole genomes.

.