Dear James:
Thanks for your reply.
For the samtools mpileup, from the resulting mpileup file, my conclusion is
that if I use the options -l (BED file) and -a at the same time, it will
output the region in the BED file even if the depths in the region are all
0. But if I just use the options -l (BED file), it will not output the
region if the depths in a region are all o, and it will output the region
if the depths in a part of a region or the whole region are not 0. Is my
conclusion right? Look forward to hearing from you!
Best
Jing
On Fri, Jul 13, 2018 at 7:26 PM, James Bonfield <j...@sanger.ac.uk> wrote:
> On Fri, Jul 13, 2018 at 06:44:30PM +1000, Jing meng wrote:
> > I run samtools mpileup and set the -d 100 (max per-file depth), and that
> is
> > the ouput information:
> >
> > [mpileup] 1 samples in 2 input files
> > <mpileup> Set max per-file depth to 8000
> >
> > Why the output (max per-file depth to 8000) is different from What I set
> > (max per-file depth to 100)?
>
> This has been fixed in develop and will be in an official release
> shortly.
>
> > Also, is the per-file depth the per-site depth?
>
> It's used to set the maximum depth of reads starting at each site, per
> input file.
>
> > I set the -d to be 100. Why I still get some records in the pileup file
> > whose depth is larger than 100 at the genomic site?
>
> The depth limit isn't really a limit, but a hint used to prevent
> slow downs when getting to extremely deep regions. Specifically it
> limits the number of reads *starting* at each site, so -d 100 will
> mean no more than 100 reads starting at position X, but another 100 at
> at position X+1 will be permitted. Assuming more than 1bp long reads
> that then gives depth 200. The reason for this logic is if we blocked
> reads at X to X+L (assuming fixed length L) then we'd get a huge drop
> in depth immediately following this, potentially to zero.
>
> The problem here is the wording of the option which implies a hard
> limit rather than as a filtering option for efficiency purposes.
>
> James
>
> --
> James Bonfield (j...@sanger.ac.uk)
> The Sanger Institute, Hinxton, Cambs, CB10 1SA
>
>
> --
> The Wellcome Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
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