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Increase read depth for MuTect?
I am wondering how I could increase the amount of reads MuTect considers in its analysis. As an example, for the same sample VarScan2's output displays DP=20862 whereas MuTect's output VCF displays DP=989. This makes it harder to compare their respective outputs.
I look forward to some answers. I have looked around quite a bit and haven't found anything concerning this.