The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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.