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Contents
Contents
BIMBAM
User Manual
Yongtao Guan and Matthew Stephens
Contents
What's new in this release version 0.99
New features
Introduction
Preliminaries: Transforming Quantitative Traits
Input file format
Genotype file format
Phased genotype file format
Mean genotype and genotype distribution file as input
Non-genotype input files
Phenotype file format
SNP location file format
Use of multiple genotype and phenotype files
The strand issue
Running
BIMBAM
Calculation of multi-SNP BFs
Calculation of imputation-based BFs
P-value calculation:
-pval
option
Specify priors:
-A -D
option
Combining studies:
-ssd -psd
option
Output Files
Single-SNP Bayes Factors:
prefix.single.txt
Multi-SNP Bayes Factors:
prefix.multi.txt
Summary of results:
prefix.summary.txt
Log file:
prefix.log
Other Options
Binary (0/1) phenotype: the
-cc
option
Restricting the multi-SNP calculations: the
-m
option
Restricting analyses to subsets of the data: the
-gene
and
-GF
option
Saving results from EM runs
Outputting imputed genotypes
Genotype data screening
Miscellaneous other options
Parallel computing version (no longer supported in version 0.99)
Bibliography
About this document ...
Yongtao Guan 2009-02-19
