BIMBAM HELP

Hello, I am trying to run Bimbam on blood stage Plasmodium falciparum SNP data. My issue is coding

I hope the attached files help with q 2. The answer to your question 1 is Yes. The answer to question

Hello I need a suggestion for analyzing my rflp data. I know all have sequencing data but I do not

Dear Yongtao, If I use a 2-SNP model, the summary file will give me a matrix of BF and a

> (1) What are the defaults for the hyperparameters -h and -p and do you > recommend trying

I did imputation on Windows XP and found an weird error: -bimbam: genotype phenotype files not match

http://quartus.uchicago.edu/~yguan/bimbam/manual/node17.html http://quartus.uchicago.edu/~yguan/

Dr. Guan, Following my previous question, I also wonder, why the p value obtained using Bimbam was

Hi, Yongtao, Based on my previous experience, the imputed SNPs for each individual may be different

I am using fastPhase for missing genotype imputation. If any one knows bout how to convert the

Hi Gaël, Bayes factor reflects change of odds ratio in light of data, ie, posterior_odds = prior_odds

Tim, That's a good question. For each SNP, after running single SNP analysis, you obtain mu (

It seems that you used genotype distribution file instead of mean genotype file for gmode 1. Please

Hi Lynne, Yes, this is a bug found in version 0.99. Thank you for reporting this. Grant On Mon, Aug

yes, trying to do all pairs of markers among 300 million is rather ambitious. This functionality was

you can estimate your local FDR for each SNP association identified by computing the posterior

You can always write a script to convert from mach format to the bimbam format. The bimbam format can

Dear all, I would like to explore 6 SNPs in one gene vs. a categorical variable, but assuming a trend

Thank you both for the input! The " chmod 755 bimbam_* " command worked, making the file

If there is a log file being generated, could you send it to me? What OS are you using? Could you

Hi all, I just wanted to let the group know that the server hosting the windows version of bimbam

Thanks to both Grant and Mat...both were helpful. Now I've got more to rattle around in my brain!

Tim, I posted the 0.99 source code on registration page of bimbam website. My gsl is 64 bit, and can

Jeremie, The Windows version for BIMBAM 0.99 is now available thank to Bertrand. You can find the

Could you help me to recreate the scenario by emailing me the files and command you used? Grant On

Hi Grant, Thank you for your reply >The bug (when imputation and permutation ran together) has

Thank you so much, For information to others, I found it in http://quartus.uchicago.edu/~yguan/bimbam

Huwaida, You have to use panel in order to do imputation. The data for hapmap panel can be downloaded

Replica watches from Officine Panerai closest to original http://gazejoin.com

basically you are correct that it will not be possible to get an accurate p value. You can proabbly