Given a multianno file (annovar's output) fix its header by adding the vcf columns (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT and SAMPLE)

fix-multianno-header.sh

#!/bin/bash

multianno=${1}

header=$(head -1 ${multianno})
fixedHeader=$(echo "${header}" \
    | sed 's/Otherinfo/VCF_CHROM/' \
    | awk '{print $0"\tVCF_POS\tVCF_ID\tVCF_REF\tVCF_ALT\tVCF_QUAL\tVCF_FILTER\tVCF_INFO\tVCF_FORMAT\tVCF_SAMPLE"}' \
)

sed -i '1 s,'"${header}"','"${fixedHeader}"',' ${multianno}