My question: How can I generate a pileup with an output of more than 8000 hits per base? I was generating pileups using the SAM tools --> Generate pileup and do not see an option to change the settings for output. In mpileup there is a variable that looks correct, -D (Output per-sample read depth) , but I cannot figure out how to adjust it. I checked the box, Output per-sample read depth, under the advanced settings but the log file generated still says the max depth was 8000.

The pileup files I generated look great but I would like to know what the true read depth is at the 8000 hit plateaus.

Any help appreciated. I'm a little out of my depth here.

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Lauren M. Oldfield
Hatfull Laboratory
Dept. of Biological Sciences
University of Pittsburgh
376 Crawford Hall
4249 Fifth Ave
Pittsburgh, PA 15260
412-624-6976