On Wed, Sep 25, 2013 at 7:27 PM, Lauren Oldfield lmo14@pitt.edu 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.
Hi Lauren,
Unfortunately this is a samtools design choice, 8000 is the coverage limit hard coded in the source code itself (see files bam_pileup.c and bam_plcmd.c), so at the very minimum it would mean manually editing the samtools source and recompiling samtools.
It would be best to ask about this on the samtools-help mailing list (CC'd), as it may be more complicated than just editing a few lines of the C code.
For the samtools folk - could this magic limit of 8000 be done via a #define to make it clearer this is a special constant, and give people just one place to change the code?
Any help appreciated. I'm a little out of my depth here.
Ha ha, good pun.
Peter