Exporting imputed genotype distribution with '-wgd' - Not all imputed SNPs are listed

[Jeremie Lebrec]

Hi,

I have found out in one of the answers posted to this list that the
option '-wgd' allows one to save the probability distribution of the
imputed genotypes. I have used it using the hapmap CEU provided on the
BIMBAM resources web page as the reference panel and some personal
test data but the 'out.genotype.distribution.txt' file only has
information for 3 SNPs. The corresponding 'out.single.txt' has BF
computed at all SNPs in my test data which includes many (>>3)
ungenotyped SNPs.

I am using BimBam 0.9.5 for Windows with the following call:

bimbam -g input/regio.geno.txt -p input/regio.pheno.txt -g resources/
hap.phased.ceu.b36.chr1.inp -p 0 -pos resources/
hap.phased.ceu.b36.chr1.pos -gene input/genefile.txt -o regio.out -i 1
-wgd

Is this a bug?

By the way, as far as I am aware, the '-wgd' option does not appear in
the manual.

Thanks in advance for your help,

Jeremie

[Yongtao Guan]

Jeremie,

Please use the new version 0.99.
And use ./bimbam -h for command detail.
I will update the manual soon.

Thank you.
Grant

--
Yongtao Guan, PhD
Postdoctoral Fellow
Dept of Human Genetics
University of Chicago
http://home.uchicago.edu/~ytguan/

[Yongtao Guan]

Jeremie,

The Windows version for BIMBAM 0.99 is now available thank to Bertrand.
You can find the link at the bottom of the registration page.
http://quartus.uchicago.edu/~yguan/bimbam/registration.html

Grant


On Thu, Feb 5, 2009 at 3:58 PM, Yongtao Guan <ytg...@gmail.com> wrote:
> Oh... you are using windows version.
> The compilation of Windows version involves another person, let me see
> what I can do.
>
> Grant
>
> On Thu, Feb 5, 2009 at 3:46 PM, <J.Le...@lumc.nl> wrote:
>> Hi Grant,
>>
>> That is a quick reply!
>>
>> I am sorry but I cannot find this version on the web. Is a Windows .exe version also available for 0.99? If so, where can I find it?
>>
>> Thanks,
>>
>> Jeremie