[Bioc-devel] Masked version of BSgenome.Hsapiens.NCBI.GRCh38?

[Hervé Pagès]

Hi,

BSgenome.Hsapiens.UCSC.hg38 is available in devel via biocLite()

   http://bioconductor.org/packages/devel/BiocViews.html#___BSgenome

and BSgenome.Hsapiens.UCSC.hg38.masked is currently propagating and
will become available in the next couple of hours.

On 02/08/2015 11:42 PM, Ulrich Bodenhofer wrote:
> Hi Hervé,
>
> Thank you for your positive reply and thanks a lot in advance for your
> efforts putting the packages together! Just that you know, I am not
> personally in desperate need for these packages. I am currently
> finishing a GWAS-related package and I thought it would be nice to
> integrate support for the latest human genome build, but I think it is
> not (yet) a must-have feature. I do not know whether there are actually
> hg38-/GRCh38-based VCF files around yet, but I'm sure it is only a
> matter of time until they are.

Yes there are. Starting with build 141, dbSNP is based on GRCh38
and they provide the usual VCF files for that build. VCF files
based on hg38/GRCh38 are going to proliferate soon so we'd better
get ready :-)

Also we already have a TxDb package for hg38 (thanks Marc!)

   http://bioconductor.org/packages/devel/BiocViews.html#___TxDb

so it makes a lot of sense to have the corresponding BSgenome packages.

Cheers,
H.

>
> Thanks and best regards,
> Ulrich
>
>
> On 02/09/2015 08:23 AM, Hervé Pagès wrote:
>> Hi Ulrich,
>>
>> I was not sure about how much demand there is for the masked BSgenome
>> packages in general so I was just waiting for someone to ask. Note that
>> the masks are typically generated from data available at UCSC so it
>> sounds that it's time to make BSgenome.Hsapiens.NCBI.hg38 and
>> BSgenome.Hsapiens.NCBI.hg38.masked available.
>>
>> I'll prepare the 2 packages in the next couple of weeks and post back
>> here when they are ready for download.
>>
>> Cheers,
>> H.
>>
>> On 02/06/2015 06:13 AM, Ulrich Bodenhofer wrote:
>>> Hi,
>>>
>>> The latest human genome build GRCh38 has been around in Bioconductor for
>>> some while (package BSgenome.Hsapiens.NCBI.GRCh38). As far as I can
>>> tell, however, there is currently no package that provides easy access
>>> to masked/unmasked regions in the genome (like there is a .masked
>>> version that wraps BSgenome objects into MaskedBSgenome objects for many
>>> other genomes, e.g. there is BSgenome.Hsapiens.UCSC.hg19.masked for
>>> hg19). Here is my question: does anybody have plans to include a
>>> package BSgenome.Hsapiens.NCBI.GRCh38.masked (or under a different name)
>>> into Bioconductor 3.1? At least I could not find anything in the current
>>> development branch.
>>>
>>> Thanks and best regards,
>>> Ulrich
>

-- 
Hervé Pagès

Program in Computational Biology
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