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Mutect2 AF calculation discrepancies
I called some targeted DNA-seq using GATK 4.0 mutect2 :
java -jar $gatk_jar Mutect2 \ -R $ref_fasta \ -I $bam \ -tumor $sample \ -L $genomic_interval_bed \ --dbsnp $dbSNP_vcf \ -O $sample"_mutect2.vcf.gz"
Works well but I've a question regarding the generated vcf. Looking at it I found some variants with calculated AF that do not reflect the number of alternate reads vs reference reads.
chr10 43597975 . C T . . DP=395;ECNT=1;POP_AF=1.000e-03;P_GERMLINE=-3.512e-04;TLOD=6.21 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1:313,6:0.112:125,6:188,0:30:80,90:60:15:0.010,0.020,0.019:0.011,1.407e-03,0.988
If I understood this line, I've 395 reads in total. 313 reference and 6 alternate looking at the AD tag. AF=0.112
First question : 313+66 != 395. Did I misinterpret the DP and AD tag ?
Second question : 6/395 != 0.112 . How is the AF tag computed ?
Did I miss something here ?