Missing Allele Balance Tag In Vcf File

Question

[Johan]

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

[Omid]

As far as I know AB= (Ref/Ref+ALT) and it is mentioned just for heterozygous variants.But for homozygous variants it is recorded zero.It was what I have seen in my out put file.

[Getting there]

I think it is the opposite AB=(ALT/REF+ALT) but I have seen it written both ways... I noticed in my VCFs if AB=1 or AB=0 it still means homozygous variant. If AB=1 it is usually an indel and if it's AB=0 it's a SNV. If AB = 0.### then it is heterozygous. It is not explained in the VCF docs. But here is a helpful snippet from a paper

"...allele balance (AB, number ALT reads/(number REF reads+number ALT reads), where ‘ALT’ and ‘REF’ reads refers to reads containing the alternate or reference base in a heterozygous SNP) between 0.2 and 0.8."

https://www.nature.com/articles/ncomms12824