BIMBAM pipeline

BIMBAM specifications

Information


Unique identifier OMICS_04401
Name BIMBAM
Alternative name Bayesian IMputation-Based Association Mapping
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A genotype file and a phenotype file
Input format TXT
Output data A log file, a single-SNP Bayes factors file, a multi-SNP Bayes factors file and a summary file
Output format LOG, TXT
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for Bayesian IMputation-Based Association Mapping

BIMBAM IN pipelines

 (4)
2016
PMCID: 5111214
PMID: 27846816
DOI: 10.1186/s12863-016-0455-5

[…] associated to the colour phenotypes. those above 99% empirical quantile for bf (bf0.99 snps) were considered to have the strongest associations. imputation of the missing genotypes was performed in bimbam v1.0 [55]., genetic differences among populations were tested using a g–test [56] and estimates of f st were obtained following the method of [57] implemented in genepop v4.2.2 [58]. to better […]

2012
PMCID: 3469421
PMID: 23071454
DOI: 10.1371/journal.pgen.1003000

[…] for all qtl mapping analyses, we used close to full genotype information for each of the 70 yri individuals, achieved by combining available datasets and imputing missing genotypes with the bimbam software [58], [87], [88] as described previously [32], [59], [60]. briefly, we built a reference panel consisting of the largest set of all 210 yri hapmap individuals and gathered genotypes […]

2011
PMCID: 3102751
PMID: 21637794
DOI: 10.1371/journal.pgen.1002078

[…] all genotypes to reference genome (b36) forward strand alleles, as subtle errors in genotype strand inference will downwardly bias replication rate estimates. additional genotypes were imputed with bimbam (v 0.99) [58], using hapmap release 27, build 36 unphased genotypes as reference panels. european american genotypes were imputed with a ceph reference panel, while african american genotypes […]

2011
PMCID: 3102751
PMID: 21637794
DOI: 10.1371/journal.pgen.1002078

[…] panels. european american genotypes were imputed with a ceph reference panel, while african american genotypes were imputed with a combined ceph and yri panel. imputation was run with default bimbam parameters, and mean imputed genotypes were recorded and used for all downstream analyses., we performed a principal component analysis (pca) based quantification of race using the african […]

BIMBAM institution(s)
Department of Statistics, University of Washington, Seattle, WA, USA
BIMBAM funding source(s)
This work was supported by NIH grant RO1 HG02585–01.

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