Increase read depth for MuTect?

ssodermanssoderman TexasMember

Hello All,

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.

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  • ssodermanssoderman TexasMember
    edited July 2015

    Ah yes there are downsampling options. By default it seems that a maximum of 1000 reads are considered. I'm now awaiting several outputs from the program with an increased downsampling parameter. :) Thank you so much for mentioning this! If this somehow doesn't fix things I will look into the quality information.

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