GenotypeGVCFs data fields missing
I'm a bit confused about some output from GenotypeGVCFs. I have run it on three GVCF files, however for the second file, some of the data specified for the format field is missing for some sites. E.g.:
25_random 152466 . T G,TG 1050.92 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-4.740e-01;ClippingRankSum=0.189;DP=58;FS=0.000;GQ_MEAN=159.50;GQ_STDDEV=176.07;MLEAC=2,1;MLEAF=0.500,0.250;MQ=58.36;MQ0=0;MQRankSum=0.053;NCC=0;QD=21.02;ReadPosRankSum=-1.890e-01 GT:AD:DP:GQ:PL 0/1:5,7,5:17:35:200,0,293,106,35,350 ./. 1/2:2,22,9:33:99:1071,284,284,747,0,911
For the other two samples, when there is no data or the genotype is not called, the other fields are still present:
1 45244823 . C A,T 173.69 . AC=1,1;AF=0.500,0.500;AN=2;DP=7;FS=0.000;GQ_MEAN=108.00;MLEAC=1,1;MLEAF=0.500,0.500;MQ=144.40;MQ0=0;NCC=2;QD=24.81 GT:AD:DP:GQ:PL ./.:0,0,0:0 1/2:0,3,4:7:99:294,158,144,122,0,108 ./.:0,0,0:0
I'm using gatk 3.2.0.
If someone could help me understand what is going on here, I'd be very grateful. I was also wondering if there is a way to report the SB field in GenotypeGVCFs?