after gatk merge gvcf to vcf; then bcftools stats, I found a result of stats lose some count

[nameOnStone]

as like title, if one line like this "chr1 11140624 . C A,* 366.64 . AC=1,1;AF=0.250,0.250;AN=4;BaseQRankSum=-8..." , in "A,*", symbol star indicate there is one sample lose REF C, So I think this line should increment indel counter, But actually Not, could you fix this problem? Thankyou

[pd3]

I don't think that would be correct. It is the same indel reported upstream, not another indel. Or maybe I am misunderstanding?