[Bioc-devel] dealing with GRCh38 build

Marc Carlson mcarlson at fhcrc.org
Mon Jul 28 19:57:23 CEST 2014

Hi Vince,

The current Homo.sapiens package/object contains a reference to an hg19 
TranscriptDb object (which makes it specific to hg19).  But you can 
easily make a custom Homo.sapiens object of your own that points to a 
custom TranscriptDb object.  Making a custom OrganismDbi object is easy 
to do and is documented in the OrganismDbi vignette:


So there nothing very fancy going on here right now.  But you can 
customize to match a build if you have made the base annotation objects 
(TranscriptDb, OrgDb etc.).


On 07/28/2014 10:37 AM, Vincent Carey wrote:
> I confirmed that the rtracklayer liftOver will work with the appropriate
> chain.  the
> remap utility seems to have some more configurability.  might be worth a
> look.
> What I need to do promptly is put the proper seqinfo on result of
> makeCurrentGwascat
> so that folks are not led astray.  We also need good marking of which build
> is in use on all our ranges, IMHO.
> On Mon, Jul 28, 2014 at 1:14 PM, Vincent Carey <stvjc at channing.harvard.edu>
> wrote:
>> I just noticed that the addresses for NHGRI GWAS catalog distribution
>> are relative to GRCh38.  Is there a plan for using Homo.sapiens with
>> selection of build?  It may not be uncommon for someone to want to
>> work with different builds.
>> What would be useful for me at this time is a simple way to get a Seqinfo
>> structure respecting GRCh38.  Also, liftOver seems to have been replaced
>> by NCBI remap.  Apparently the new build can also be called hg38, and a
>> chain
>> file exists, so rtracklayer liftOver utility should still succeed.
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