Please take a look at this post: Changing Chromosome Notation On Vcf

A simple Regex should suffice for the variant lines, but you may wish to address the header with more caution - you'll need to change the location of the reference and the details on the contig lines.

EDIT: Or, use this to overcome the problem where ref with contigs 1,2,3... might differ from the ref with contigs chr1,chr2,chr3... This might prove safer in the longer run.