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@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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