[BioC] pileupAsGRanges depth limit

[Martin Morgan]

On 12/17/2012 03:12 AM, Mark Dunning wrote:
> Hi all,
>
> I'm running the pileupAsGRanges function from ggbio, and just
> wondering if there was a limit to the depth it reports? I have
> targeted sequencing data and expect many thousands of reads per base
> but the depth seems to be around 250?

Hi Mark --

applyPileups takes a 'PileupParam' argument, which has maxDepth=250L as an 
argument, so maxDepth = .Machine$integer.max would get you everything.

The ... arguments of pileupAsGRanges gets passed to PileupParam, so I think you 
can add maxDepth=.Machine$integer.max to pileupAsGRanges().

Martin

>
>> pgr[3:5,
> + ]
> GRanges with 3 ranges and 7 metadata columns:
>        seqnames             ranges strand |         A         C         G
>           <Rle>          <IRanges>  <Rle> | <integer> <integer> <integer>
>    [1]    chr17 [7577489, 7577489]      + |         1         0       249
>    [2]    chr17 [7577490, 7577490]      + |         0         6       245
>    [3]    chr17 [7577491, 7577491]      + |         1       250         0
>                T         N     depth                     bam
>        <integer> <integer> <numeric>             <character>
>    [1]         0         0       250 CleanedBams/FLD0097.bam
>    [2]         0         0       251 CleanedBams/FLD0097.bam
>    [3]         1         0       252 CleanedBams/FLD0097.bam
>
>
> I think that samtools mpileup has a default depth of 250, so is it the
> case that the applyPileup function is using the same limit, and it is
> possible to change it?
>
> Mark
>
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