GATK version used: v4.1.9.0

I have a series of WES samples and ran the somatic mutation calling pipeline (Mutect2). Next, I took the union of all the reported variants. What I would like to know is the coverage on the REF and ALT allele for each variant and for all samples. 

I thought I might be able to do this running VariantAnnotator on the merged VCF. Specifically, for a VCF file where variants from sample A, B and C were merged, I ran the command:

gatk VariantAnnotator -V A_B_C_merged.vcf.gz -I A.bam -I B.bam -I C.bam --output VA_ABC.vcf -A Coverage -A DepthPerAlleleBySample -A ChromosomeCounts

It seems that I only get coverage (and other info) when at least 1 read maps to the ALT allele. This even holds for regions with high coverage. 

For example:

bcftools query -i 'INFO/DP > 500' -f '%CHROM\t%POS\t%ALT\t%REF\t[%DP\t]\n' VA_ABC.vcf returns:

CHR   POS          REF   ALT   A   B   C
chr1 11668809     G        A      .      .    311
chr1 16625831     A        G      .      .     81
chr1 16628668     T        C      .    201  .
chr1 16686072     C        T     164   .    .
chr1 16760342     T        G     779   .    .
chr1 16930115     A        C      274   .    .
chr1 21885008     T        C     119    .    .
chr1 58056429 CTAACT C      .      .    183
etc.

For variants with AC==2 (AC==3) I do see the coverage on both (all 3) the samples.

My question is: How do I get coverage info for all variants, even if all reads map to the REF allele for some samples? Is VariantAnnotator the right tool? Should I use a different settting (I checked, but may have overlooked)? Or is a different tool maybe more appropriate?

Thanks in advance!

Wout