Hi all,
I have a question regarding the variants' AF value reported in the normal sample when using Mutect2 in paired mode.

I have noticed that AF in the normal sample is never 0, even in those cases where AD says that there are 0 reads with ALT.

For example, for this deletion (first INFO column is for normal sample and second tumoral sample):

chr15    65150921    .    GAAAAGCCATGTTTGTTTTTTTAAAATAAAAAATGGAGGTAAACATGATCTTTAAAATCA    G    .    PASS    AS_FilterStatus=SITE;AS_SB_TABLE=24,75|5,36;DP=162;ECNT=1;GERMQ=66;MBQ=38,40;MFRL=182,215;MMQ=60,60;MPOS=35;NALOD=1.5;NLOD=8.39;POPAF=6;TLOD=160.96    GT:AD:AF:DP:F1R2:F2R1:FAD:SB    0/0:41,0:0.032:41:1,0:15,0:31,5:10,31,0,0    0/1:58,41:0.459:99:11,9:19,12:45,38:14,44,5,36

In the normal sample:

AD = 41,0

AF = 0.032

What I see in igv: 0

Another example for a SNV:

chr1    13391966    .    A    G    .    PASS    AS_FilterStatus=SITE;AS_SB_TABLE=21,13|7,6;DP=49;ECNT=1;GERMQ=66;MBQ=20,40;MFRL=147,256;MMQ=60,40;MPOS=19;NALOD=-1.687;NLOD=3.03;POPAF=6;TLOD=52.12GT:AD:AF:DP:F1R2:F2R1:FAD:SB    0/0:34,1:0.074:35:3,0:21,1:24,1:21,13,0,1    0/1:0,12:0.93:12:0,5:0,6:0,12:0,0,7,5

In the normal sample:

AD = 34,1

AF = 0.074

What I see in igv: 0.28

How is AF calculated? Is it calculated from the reallignment Mutect2 does?

Should I recalculate it form AD? Because I would expect AF to be 0 in the normal sample for somatic mutations.

Thanks in advance.

Francisco

REQUIRED for all errors and issues:
a) GATK version used: 4.3.0.0
b) Exact command used: 

gatk --java-options "-Xmx36g" Mutect2 \
        --input WES_FD_N_1-1.converted.cram --input WES_FD_T_1-1.converted.cram \
        --output WES_FD_T_1_vs_WES_FD_N_1.mutect2.vcf.gz \
        --reference GRCh38.d1.vd1.fa \
         \
         \
        --intervals chr1_12081-12251.bed \
        --tmp-dir . \
        --f1r2-tar-gz WES_FD_T_1_vs_WES_FD_N_1.mutect2.f1r2.tar.gz --normal-sample WES_FD_N_1 --genotype-germline-sites