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Quality value in Unified Genotyper, haploid option
I am attempting to produce consensus genome sequences from haploid Drosophila embryos sequenced to 30x coverage on the Illumina HiSeq, and when I use Unified Genotyper with the haploid (ploidy 1) option and EMIT_ALL_SITES, I get quality values of 3.01 for all sites that match the reference. Here are a few lines of my output vcf:
1 632 . A . 3.01 LowQual DP=250;DS;MQ=55.47;MQ0=0 GT .
1 633 . A . 3.01 LowQual DP=250;DS;MQ=55.49;MQ0=0 GT .
1 634 . G . 3.01 LowQual DP=250;DS;MQ=55.10;MQ0=0 GT .
1 635 . G . 3.01 LowQual DP=250;DS;MQ=55.48;MQ0=0 GT .
1 636 . A . 3.01 LowQual DP=250;DS;MQ=55.94;MQ0=0 GT .
1 637 . T C 735 . AC=1;AF=1.00;AN=1;BaseQRankSum=-0.939;DP=250;DS;Dels=0.00;FS=0.990;HaplotypeScore=90.4026;MLEAC=1;MLEAF=1.00;MQ=54.72;MQ0=0;MQRankSum=2.513;QD=2.94;ReadPosRankSum=0.118;SB=-4.345e-03 GT:AD:DP:GQ:MLPSAC:MLPSAF:PL 1:126,123:250:99:1:1.00:765,0
1 638 . A . 3.01 LowQual DP=250;DS;MQ=54.09;MQ0=0 GT .
1 639 . T . 3.01 LowQual DP=250;DS;MQ=54.30;MQ0=0 GT .
1 640 . G . 3.01 LowQual DP=250;DS;MQ=54.50;MQ0=0 GT .
1 641 . A . 3.01 LowQual DP=250;DS;MQ=54.39;MQ0=0 GT .
1 642 . C . 3.01 LowQual DP=250;DS;MQ=53.83;MQ0=0 GT .
Since I am producing a consensus from the VCF output, I really need some quality value for all called sites, both variable and invariable. Is there any way to do this in GATK?