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

Ulrich Bodenhofer bodenhofer at bioinf.jku.at
Mon Feb 9 08:42:44 CET 2015

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.

Thanks and best regards,

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

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