Base Quality Recalibration With Low Frequency Variants

Hi I'm working on calling low frequency heteroplasmic variants in the mitochondrial genome, using WGS data. My data is high coverage (~2000x), and heteroplasmic variants might be represented on as few as 10 reads. Am I correct that BaseRecalibrator will treat low frequency haplotypes as sequencing error in this case and reduce Phred scores for these reads? If so, is BQSR not appropriate for this data?

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