Subset a Vcf

I need to decorticate the #CHROM and #POS of a vcf, ie. to change them with new fields. I think I can arrange it on R.

But, before that, I must filter 500 variants out of 46K.

Some are just contigs, others are POS within a contig which don’t suit our expectation.
I have an idea of using vcftool for the latter task, but the panoply of commands (ancd required inputs) confuses me.

Can someone please shed me a light?