[Genome] Haplotype data of HapMap - ENCODE regions

[Makoto Shimada]

Heather:
Thank you so much for your prompt reply.
I understand and I am inspecting the following directory, 
http://www.hapmap.org/downloads/phasing/2005-03_phaseI/ENCODE/ .  
This looks suitable data for my intention.

I would like to ask further question about this data.  
The directory “/downloads/phasing” contains two subdirectories, 
“2005-03_phaseI/“and “2006-07_phaseII/.”  
Do the dates (2005-03 & 2006-7) in these subdirectories represent fixed
date of genotype data used?  If so, these two phased data have been
derived from following two genotype data, respectively?
http://www.hapmap.org/genotypes/
2005-03_16a_phaseI/ 
2006-07/ 
Could you tell me whether I understand correctly?

-- 
Makoto Shimada <mashimad at jbic.aist.go.jp>

On Thu, 5 Apr 2007 09:14:45 -0700 (PDT)
Heather Trumbower <heather at soe.ucsc.edu> wrote:

> Makoto:
> 
> You are indeed looking for HapMap data which is available from 
> http://www.hapmap.org.
> 
> Specifically, genome-wide phasing data is available by going to
> http://www.hapmap.org/ and clicking on 'Bulk Data Download' under
> 'Project Data'.
> 
> This takes you to http://www.hapmap.org/downloads/index.html.en.
> You can then click on 'Phasing Data' under ('Bulk Data').
> 
> There are two directories there.  Phase II includes all of Phase I.
> The documentation for the Phase II data is
> http://www.hapmap.org/downloads/phasing/2006-07_phaseII/00README.txt.
> 
> You may also be interested in the 'ENCODE Project' link which is available 
> from the main page in the 'Project Data' section.
> 
> As far as I know, the ENCODE re-sequencing data have not been phased 
> separately.
> 
> The HapMap mailing list -- help at hapmap.org -- may be able to provide more 
> information.
> 
> Heather Trumbower
> UCSC Genome Bioinformatics Group
> 
> 
> On Thu, 5 Apr 2007, Makoto Shimada wrote:
> 
> > To whom it may concern,
> >
> > I wonder if I could have public haplotype data around genic regions by
> > re-sequencing of some human population containing several individuals.
> > I guess that there are haplotype data of HapMap - ENCODE regions, which
> > were re-sequenced in 48 unrelated individuals.
> > Could you tell me where those are available?
> >
> > I know how to get genotype data in each SNP site from following site,
> > http://www.hapmap.org/downloads/genotypes/  .
> > However these are not done haplotype inference (phasing).
> > I would like to have (phased) haplotype data.
> >
> > I attached archives relating this subject.
> >
> > With my best,
> > Makoto
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Makoto Shimada, Ph.D.
> > Integrated Database Team
> > Japan Biological Information Research Center
> >
> > AIST Tokyo Waterfront Bio-IT Bldg 7F
> > 2-42 Aomi, Koto-ku,
> > Tokyo, Japan, 135-0064
> > TEL: +81-3-3599-8537, FAX: +81-3-3599-8801
> > E-mail: mashimad at jbirc.aist.go.jp
> > http://www.jbirc.aist.go.jp/idt/index_e.html
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>