Alt allele depth in FORMAT column missed in GenotypeGVCFs output?

[xiucz]

• version GATK4.2.6.1

Hi, When I use the following command to genotype a single g vcf file, the output alt depth(ref depth is ok) in the FORMAT column are missing.

gatk GenotypeGVCFs -R ucsc.hg19.fasta -verbosity ERROR -all-sites true  -stand-call-conf 0 --dbsnp dbsnp_138.hg19.vcf  -V 0003.g.vcf -O 0003.4.2.6.1.vcf 

For example, AD:DP 2,1013:1116, 1116 is for the total depth(DP), and 2,1013 is for the ref depth, however, the alt allele depth is missing. is this a bug? Or did I miss something?

##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

#input 
chr19	45923653	.	A	G,<NON_REF>	31988.06	.	BaseQRankSum=-1.361;DP=1149;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=0.000;RAW_MQandDP=4136400,1149;ReadPosRankSum=-1.250	GT:AD:DP:GQ:PL:SB	1/1:2,1013,101:1116:99:32002,2966,0,32008,3040,32082:1,1,538,576

#output 
chr19	45923653	rs11615	A	G	31988.06	.	AC=2;AF=1.00;AN=2;BaseQRankSum=-1.361e+00;DB;DP=1149;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.00;QD=31.52;ReadPosRankSum=-1.250e+00;SOR=0.764	GT:AD:DP:GQ:PL	1/1:2,1013:1116:99:32002,2966,0

Best, xiucz