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Not all FORMAT fields are being emitted
I' am using the CombineVariants tool from GATK after calling mutations with Mutect. To simplify my case I will show three samples and one variants. Specifically, I encounter the problem where for the VCF file for each individual sample has the AD field, but the combined file does not. Here is the variant information for the three samples:
1 5070218 . T TAGATTATTGATGATTTA . PASS ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=0.00;TLOD=10.71 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:10,4:0.2:1:0:.:248,27:5:5
1 5070218 . T TAGATTATTGATGA . PASS ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=0.00;TLOD=19.49 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:5,5:0.5:5:0:.:140,130:1:4
1 5070218 . T GT . PASS ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=0.00;RPA=6,7;RU=T;STR;TLOD=13.13 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:100,13:0.115:6:7:.:2941,405:38:62
Then I run the following,
java -jar ~//GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar -T CombineVariants --variant HL-WES-103.mutect.vcf --variant HL01.mutect.vcf --variant HL-WES-87.mutect.vcf -R ~/GRCm38/Mus_musculus.GRCm38.dna.primary_assembly.fa -o test.vcf
The output is
1 5070218 . T TAGATTATTGATGA,GT,TAGATTATTGATGATTTA . PASS AC=1,1,1;AF=0.167,0.167,0.167;AN=6;ECNT=1;HCNT=2;MAX_ED=.;MIN_ED=.;NLOD=0.00;RPA=6,7;RU=T;STR;set=Intersection GT:AF:ALT_F1R2:ALT_F2R1:QSS:REF_F1R2:REF_F2R1 0/1:0.5:5:0:140,130:1:4 0/3:0.2:1:0:248,27:5:5 0/2:0.115:6:7:2941,405:38:62
Notice how the AD field is missing? Is this a bug?