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. Peter ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/