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.
Another way of doing this by using bcftools v1.9:

    echo "1 chr1" >> chr_name_conv.txt
    echo "2 chr2" >> chr_name_conv.txt
    bcftools annotate --rename-chrs chr_name_conv.txt original.vcf.gz | bgzip > rename.vcf.gz
