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.
    awk '{gsub(/^chr/,""); print}' your.vcf > no_chr.vcf

Should get rid of the chr

    awk '{if($0 !~ /^#/) print "chr"$0; else print $0}' no_chr.vcf > with_chr.vcf

Will add the chr to the VCF without chr.

You can use either command depending on how the chromosomes are named in your reference.

Regarding preference of tools, if you plan to do downstream processing with GATK, I'd suggest sticking with GATK CombineVariants for consistency.
