Help regarding variant filtration and variant density calculation

Question

[mirza]

I have completed variant calling and annotation and I need help with the following analysis. Is it possible to do the following analysis with my vcf files using vcftools or snpsift or bedtools?

1. Count the heterogygous SNPs according to different class i.e. C/T; T/C; etc
2. Calculate variant density (for both SNPs and Indels, seperately) in different regions i.e. exonic region, intronic region, genes, intergenic region?
3. Is it possible to filter variant data and generate separate .vcf files on the basis of the region annotated i.e. I want to generate separate .vcf files for variants in exon, intron, intergenic region?

Please guide me to the right command.