Maybe How to calculate the number of SNPs in each sample in a multi vcf file helps?

For the missing variants, I have created this simple awk script to count the number of ./. genotypes per sample, let me know if it works.

NR==1 {
    for (i=10; i<=NF; i++) {
        f[i] = $i
    }
}
{
    for(i=10; i<=NF; i++) {
        if ($i ~ /\.\/\./){
            b[i]++}}
    }
END {
    for(i=10; i<=NF; i++)
        printf "%s %s\n", f[i], b[i]
}

Save the previous code in a file named sc.awk (for example), and run it using:

awk -f sc.awk multi_sample.vcf

I think bcftools stats -S samples.txt file.vcf provides this kind of information among others