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Bug Report: mean genotype input (-gmode 1) produce erroneous results
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Trefoil  
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 More options Aug 27 2009, 10:08 pm
From: Trefoil <xueyaz...@gmail.com>
Date: Thu, 27 Aug 2009 19:08:39 -0700 (PDT)
Local: Thurs, Aug 27 2009 10:08 pm
Subject: Bug Report: mean genotype input (-gmode 1) produce erroneous results
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Hi BIMBAM developers,

To briefly describe the problem:

I first ran bimbam [latest linux version] on my chip data and use
hapmap as reference panel to simultaneously produce imputed genotypes
and do association test. Then I took the resulting mean genotypes as
input (-gmode 1) but found I could no longer reproduce the previous
association results. During the execution time, screen output said
many SNPs had been removed because their maf<0, and the
resulting .snpdata.txt file indicated that most SNPs have maf
approaching zero; both of which were clearly not the case for my data.
When I tried to feed bimbam with genotype distribution (-gmode 2), no
such problem was found. So I think it is a bug for "-gmode 1" input
mode.

I can send my data to you if necessary to help debugging. Thanks!

Xueya


 
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Yongtao Guan  
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 More options Aug 27 2009, 11:43 pm
From: Yongtao Guan <ytg...@gmail.com>
Date: Thu, 27 Aug 2009 22:43:53 -0500
Local: Thurs, Aug 27 2009 11:43 pm
Subject: Re: Bug Report: mean genotype input (-gmode 1) produce erroneous results
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It seems that you used genotype distribution file instead of mean
genotype file for gmode 1.
Please send me the log file if it's not the case.
Thanks,
Grant

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

 
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