The result of Mutect BAM and vcf is different.

I got some vcf result using mutect. but I have some question about the result.

  1. the Allele frequency in vcf is so strange.
    for example, the below is my result.
    chr4 1809127 . C T . clustered_events;panel_of_normals;triallelic_site ECNT=2;HCNT=2;MAX_ED=17;MIN_ED=17;NLOD=0.00;TLOD=24.52 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:109,29:0.078:0:0:.:270,103:0:0

the number of ref, alt genotype is 109, 29, but why alllele frequency is 0.078 ?
is it correct that AF 0.21 ?? (29 / (109+29))
I don't understand.

  1. And, the base count of Mutect bamout is different with mutect vcf result.
    below is vcf result,
    chr12 93966398 . A C . PASS ECNT=1;HCNT=20;MAX_ED=.;MIN_ED=.;NLOD=0.00;TLOD=12.85 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:90,32:0.256:0:0:.:1740,509:0:0

below is basecount (gatk) result of mutect bamout file.

chr12:93966398 186 93.00 58 A:38 C:20 G:0 T:0 N:0 128 A:96 C:32 G:0 T:0 N:0

vcf result indicate ref(A) =90 and alt(C)=32, but mutect bamout file indicate different basecount (A=96, C=32).
why is the number of basecount difference between vcf and mutect bam?

please answer my question.

thanks.

yh

ps. I used mutect2 and gatk3.6(DepthOfCoverage)

Answers

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