[BioC] pileupAsGRanges depth limit

[Mark Dunning]

Hi Martin,

Thanks for the info. I managed to work it out in the end. The tip
about .Machine$integer.max  is useful to know!

Is it possible for the function to return insertions / deletions at
each position, or just base counts?

Mark

On Mon, Dec 17, 2012 at 5:22 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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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>
>
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