On Wed, Sep 25, 2013 at 7:27 PM, Lauren Oldfield <lm...@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.

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