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.
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
Hi Lauren,
You could try to apply the following patch which sets the limit from 8.000 to 1.000.000:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=671524
Index: bam2depth.c =================================================================== --- bam2depth.c (revision 995) +++ bam2depth.c (working copy) @@ -80,6 +80,7 @@
// the core multi-pileup loop mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization + bam_mplp_set_maxcnt(mplp,1000000); // set maxdepth to 1M n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads (internal in mplp) while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position
Best
-Dominique
On Thu, Sep 26, 2013 at 6:14 AM, Peter Cock p.j.a.cock@googlemail.comwrote:
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
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Dominique Belhachemi -
Lauren Oldfield -
Peter Cock