Question: Missing Allele Balance Tag In Vcf File
gravatar for Johan
6.3 years ago by
Johan800 wrote:

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
gatk allele • 2.4k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 6.3 years ago by Johan800

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.

ADD REPLYlink written 6.0 years ago by Omid530
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