my two VCF files have different alternate allele at the same position as i have called the variants using two different callers. When i run combine Variants on the both my GT field is not updated properly. AD field is also not updated properly but i ran Variant Annotator and that fixes that issue.
chr1 87708015 rs58006838 C T 145.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.479;DB;DP=14;Dels=0.00;FS=0.000;HaplotypeScore=3.9299;MLEAC=1;MLEAF=0.500;MQ=68.54;MQ0=0;MQRankSum=-1.109;QD=10.41;ReadPosRankSum=0.925 GT:AD:DP:GQ:PL 0/1:3,9:14:37:174,0,37
chr1 87708015 . C A . PASS AN=2;DP=4;NS=1 GT:AD:DP:GQ 0/1:2,2:4:8.42
Merged VCF file:
chr1 87708015 rs58006838 C T,A 145.77 PASS AC=1,0;AF=0.500,0.00;AN=2;BaseQRankSum=-1.479;DB;DP=18;Dels=0.00;FS=0.000;HaplotypeScore=3.9299;MLEAC=1;MLEAF=0.500;MQ=68.54;MQ0=0;MQRankSum=-1.109;NS=1;QD=10.41;ReadPosRankSum=0.925;set=Intersection GT:AD:DP:GQ **0/1**:3,9,2:14:37
java -jar $gatk/2.7-1-g42d771f/GenomeAnalysisTK.jar -T CombineVariants -V one.vcf.gz -V two.vcf.gz -o test.vcf -R $ref
Is this a known limitation or a bug?