Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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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