I have a small plink file and a very large VCF that I need to use as input for an analysis. The analysis needs the chrom designations in these files to be the exact same. 

The VCF have 'chr' prefix in the #CHROM col. I know how to change this in the VCF, but it sets back my pipeline several days. Id rather modify the PLINK file.

I tried using PLINK `--update-chr` and providing a file with the chr prefix like this:

    chr1:2700157:G:A chr1
    chr1:2700163:G:A chr1
    chr1:2703633:A:G chr1

but checking the resulting bim file seems to show this does not seem to add the chr prefix, even though it says something along the lines of : `--update-chr: 331246 values updated`. Is this possible in PLINK or do I just have to bite the bullet and wrangle the VCFs?
You’re looking for the —output-chr (https://www.cog-genomics.org/plink/2.0/data#irreg_output ) flag.