Yes, gladly. Thank you for taking time to help me. Here is the exact line of R
code where we build the samtools command (the file to be tested is added later):
args <- paste("mpileup -ERI", #Redo Baq, ignore readgroups, and skip indels
"-f", refFasta(param),
"-C 50",
"--min-MQ", minMapQuality(param),
"--min-BQ", minBaseQuality(param),
"--region", as.character(chrRange, ignore.strand=TRUE))
As you can see, we use the BAQ score to filter. We have tried to implement it
without BAQ (using Rsamtools) and found it negatively affected our results.
> On Aug 23, 2019, at 4:53 PM, Martin Morgan <mtmorgan.b...@gmail.com> wrote:
>
> can you provide an example of the samtools command line that you evaluate?
>
> On 8/23/19, 6:11 PM, "Bioc-devel on behalf of Jonathon Hill"
> <bioc-devel-boun...@r-project.org on behalf of jh...@byu.edu> wrote:
>
> I had not until today. I spent the afternoon looking at the possibility,
> and it looks like it would be beyond my lab’s skills. We do not have anyone
> comfortable in C, as we do everything in R. The problem is that we need to
> get the results of the mpileup command with BAQ score. Although it has a
> pileup command, the Rsamtools implementation does not include the ability to
> retrieve the BAQ score as far as we can tell, so we had to fall back on
> making a system call to Rsamtools and reading in the results. Using Rhtslib
> is intriguing, but it looks like we would need several header files in
> Samtools as opposed to htslib and then implement our own C function. Again,
> we do not have anyone that could do this. We are scientists, not programmers.
> Am I correct on what it would require? Do you know of any other alternatives?
>
> Jonathon
>
>> On Aug 23, 2019, at 12:22 PM, Pages, Herve <hpa...@fredhutch.org> wrote:
>>
>> Hi Jonathon,
>>
>> Have you considered depending on Rhtslib? See
>> https://bioconductor.org/packages/Rhtslib
>>
>> Rsamtools itself is implemented on top of Rhtslib. Note that other
>> Bioconductor packages (e.g. DiffBind, deepSNV, BitSeq, qrqc, QuasR,
>> seqbias, TransView, etc...) use Rhtslib internally to implement features
>> not implemented in Rsamtools.
>>
>> H.
>>
>> On 8/23/19 11:05, Jonathon Hill wrote:
>>> Hi,
>>>
>>> I am working through the process of submitting a new package (MMAPPR2). We
>>> are having a problem with the build failing, because our package requires
>>> Samtools installed. We cannot use Rsamtools, as we depend on features not
>>> implemented in the package. How do we resolve the issue? What is the policy
>>> for system dependencies? We have samtools listed in the DESCRIPTION and
>>> installation instructions in our README, but I am sure that is not enough
>>> to get it installed on the Build and Check servers.
>>>
>>> Thanks,
>>>
>>> Jonathon Hill
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=AEKZKMjjFTbu5U_zn0bacvzv69lx_S5s7Yb6dSOXbJs&s=s5EMLCdAbnqgXWs3_-Sxm52Zuc3pqFirWz7z3ymBruU&e=
>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpa...@fredhutch.org
>> Phone: (206) 667-5791
>> Fax: (206) 667-1319
>
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