Description:
For comments and suggestions for using BIMBAM (Bayesain IMputation Based Association Mapping).
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haplotype analysis
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Hello I need a suggestion for analyzing my rflp data. I know all have sequencing data but I do not sequencing facility and budget. It may more basic for you but I am newbe. I have PCR-RFLP data for un related 100case and 100 control subjects. I do not have parental genotypes. I analyzed four polymorphism by four restriction endonuclease within the same gene in individuals with a particular disease and control subjects.... more »
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aborted runs and problems with multiSNP utility
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Hello,
I am a new BIMBAM user and am trying to use the program to test for
phenotypic associations within a candidate gene region and to evaluate
evidence for multiple causal mutations within that gene. I have ~800
SNPs genotyped in 90 individuals. I have been able to run single SNP
analyses and multi-SNP analyses up to L=3, but anything greater than... more »
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genotype phenotype files not match
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I did imputation on Windows XP and found an weird error:
-bimbam: genotype phenotype files not match
and the log file as below.
...test_batch.TXT
...
Command used:
./bimbam -g Ht.geno_Chr1_1.txt -p Pheno6923.txt -pos Ht.pos_Chr1_1.txt
-g hap.phased.cnj.b36.chr1.inp -p 0 -pos Panel.pos_Chr1_1.txt -wmg 1 -... more »
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p value result
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Dr. Guan, Following my previous question, I also wonder, why the p value obtained using Bimbam was different from the one using haploview? Rika
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imputation
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Hi Dr. Guan, I tried to use your software. It worked for calculating p value. But I did not know how to run imputation in using hapmap data in my genotyping data. Could you guide me how to do it? Thanks. Rika
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MPI version of BIMBAM
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Hi, Yongtao, How are you? I am trying to use BIMBAM to do the imputation for a group of patients conditioning on the references from HAPMAP. Since we have many patients, I'll try to use the parallel version of BIMBAM. We have a Linux cluster in house. My system admin already installed the MPI version of BIMBAM. I have several questions for you.... more »
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file conversion
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I am using fastPhase for missing genotype imputation. If any one knows bout how to convert the fastPHASE output to other formats like plink, hapmap, linkage or any other format.
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significativity rate in Bimbam
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Hi, I use your interesting software on a single quantitative traits, I have generated some results and I am wondering if a score of +3 could be significative or if I would except higher score ( > +30...) to detect a real significativity? Many thanks! Gaël
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Percentage of variation accounted for
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Hi all:
I am working with a couple of quantitative geneticists who are seeing
output from BimBam for the first time (they have both used regression-
based methods extensively in the past). One question that I have not
been able to answer is whether Bimbam gives us some measure of the
percentage of variability (of the phenotype) that each SNP... more »
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