for i in {1..22} X Y MT
do
echo "chr$i $i" > chr_name_conv.txt
bcftools annotate --rename-chrs chr_name_conv.txt Schrodi_IL23_IL17_combined_RECAL_SNP_INDEL_variants.VA.chr$i.vcf.gz -Oz -o Schrodi_IL23_IL17_combined_RECAL_SNP_INDEL_variants.VA.chr$i.Minimac4.vcf.gz
tabix -p vcf Schrodi_IL23_IL17_combined_RECAL_SNP_INDEL_variants.VA.chr$i.Minimac4.vcf.gz
done

I had this problem before and I was able to fix it while running some filters to the file. If you are performing any sort of filtering on those VCF files you could use:

sed 's:chr::g'

Example:

vcftools --gzvcf sample.vcf.gz --keep sample_list.txt --mac 1 --recode-to-stream | sed 's:chr::g' | bgzip -c > new_sample.vcf.gz

Next to the above answers, this resource might be helpful: mappings between common notations (UCSC, Ensembl, Gencode) https://github.com/dpryan79/ChromosomeMappings

You can use this together with

awk 'NR==FNR{map[$1]=$2;next} { for (i=1;i<=NF;i++) $i=($i in map ? map[$i] : $i) } 1' mapping_file.txt input.vcf > output.vcf

to batch rename between common chromosomal notations.

To summarize the answers people wrote before, if you have a bunch of vcf files, you don't want and need to know which has 'chr', neither use additional software. just run this in a shell script to add 'chr':

cat ${input_vcf} | grep '#' | awk '{ if(match($0,/(##contig=<ID=)([1-9].*|MT.*|X.*|Y.*)/,m)) print m[1]"chr"m[2]; else print $0}' > ${ouput_vcf}
cat ${input_vcf} | grep -v '#' | awk '{if(match($0,/^chr*/)) print $0; else print "chr"$0}' >> ${ouput_vcf}

To run it faster but not safely (jump skip the file if is correct) (suppose the vcf file is not self-contradictory),

if  [ $(cat ${input_vcf} | grep '##contig=<ID=[^G]' |  sed -n '1p' | cut -c14) != c ]; then

    # catch the non-contig header lines
    cat ${input_vcf} | grep '##' | grep -v '^##contig=<ID=[1-9XYM]'  >${ouput_vcf} &&

    # catch the contig header lines and fix it
    cat ${input_vcf} | grep '##' | grep '^##contig=<ID=[1-9XYM]' | sed 's/##contig=<ID=/##contig=<ID=chr/g' >>${ouput_vcf} &&

    # catch the column name line
    cat ${input_vcf} | grep -v '##' | grep '#' >>${ouput_vcf} &&

    # catch the variant record lines
    cat ${input_vcf} | grep -v '#'  | awk '{print "chr"$0}'  | sort -k1,1 -k2,2n >>${ouput_vcf}

fi

Update: fixed the detail, and you can copy to your ~/.bashrc now.