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,
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
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