Dear All
I have a combined VCF file of few individuals. In this VCF instead of having normal CHR1, chr2 notions for chromosomes it is having the chromosome information as 

    gi|996703411|ref|NW_015379183.1|, gi|996703411|ref|NW_015379175.1

In this notion `NW_015379183.1` corresponds to a specific Chromosome. The same is true for its positions, If I have the chromosome numbers for all `gi|996703411|ref|NW_015379183.1|` sort of notions how I can replace the chromosome names to the original names.
use `bcftools annotate` https://samtools.github.io/bcftools/bcftools.html

with 

>  --rename-chrs file
>     rename chromosomes according to the map in file, with "old_name new_name\n" pairs separated by whitespaces, each on a separate line.