Dear gatk community,
for QC I was extracting the MBQ values of my somatic variantc calls from Mutect2 (gatk/18.104.22.168, tumor-normal mode + FilterMutectCalls, from INFO column of VCF). I assumed MBQ column is giving median base quality of ref and median base quality of alt allele (seperated by comma), meaning it gives me the median of all phred scaled sequencing base qualities at the variant position of all reads considered for the ref or alt allele. Is this right?
I am asking, because some of my data shows significant differences between MBQ distributions of ref and alternative alleles, which I cannot reproduce if I extract variant and reference reads with gatk PrintReads and extract the median base qualities manually.
Thank you very much for clarifying the exact derivation of MBQ values given in the INFO column of Mutect2 VCFs.
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