I have a problem with my vcf files.
I have called SNPs using the GATK UnifiedGenotyper with the AlleleBalance annotator. For some of the SNPs the allele balance has been annotated, and for others it hasn't. (See the example below) I would really appreciate any help in understanding why this is the case.
chr5 112176559 rs866006 T G 2598.39 PASS **AB=0.502;AC=1**;AF=0.50;AN=2;BaseQRankSum=-9.353;DB;DP=329;Dels=0.00;FS=1.005;HRun=0;HaplotypeScore=24.1819;MQ=32.65;MQ0=18;MQRankSum=-8.933;QD=7.90;ReadPosRankSum=-0.599 GT:AD:DP:GQ:PL 0/1:164,163:329:99:2628,0,3234 chr5 112176756 rs459552 T A 88430.88 PASS **AC=2**;AF=1.00;AN=2;BaseQRankSum=3.447;DB;DP=2419;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=30.4979;MQ=34.64;MQ0=100;MQRankSum=-3.456;QD=36.56;ReadPosRankSum=-2.099 GT:AD:DP:GQ:PL 1/1:5,2409:2419:99:88431,6901,0