There are two VCF files that I like to merge them, using GATK or VCFtools. The problem is, they have different chromosomal notation, one has Chr, the other does not. This question could be similar to [this one](/p/13462/)

Is there any quick awk/sed commands that you suggest ?! Also I appreciate if you make comment, which of these two (GATK/VCFtools) is more reliable for this task.
Give a statistical geneticist an awk line, feed him for a day, teach a statistical geneticist how to awk, feed him for a lifetime... check out this page for find and replace using awk:

http://awk.info/?awk1line