Question: Generating Pileup With Max Depth Greater Than 8000?
4.7 years ago by
Lauren Oldfield • 10
Lauren Oldfield • 10 wrote:
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. -- Lauren M. Oldfield Hatfull Laboratory Dept. of Biological Sciences University of Pittsburgh 376 Crawford Hall 4249 Fifth Ave Pittsburgh, PA 15260 412-624-6976
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