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GATK3 MuTect2 AF calculation

jmoajmoa koreaMember

Dear GATK developers.

I've run GATK3 MuTect2 with Tumor only mode and encountered following INDEL:
chr12 133218878 . C CAGCCAGAGCAGGTGGGGCCTCCTGTGCCCTCGGGAATCTGAAT . clustered_events;homologous_mapping_event ECNT=6;HCNT=7;MAX_ED=23;MIN_ED=7;TLOD=45.92 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:653,0:0.043:0:0:.:19476,0:308:345

As you can see in the AD field, alt allele depth is zero. However, AF:0.043.
I'm aware that AD field only represent informative reads so AD can be zero.
I'm curious about two things:
1. How does MuTect2 call variants if there is no informative reads? Does it use all the reads(informative + uninformative) to call variants and just indicate only informative reads in AD field?
2. Is there a flag or metric in vcf which indicate the quality of variant due to uninformative reads?

Thank you.


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