BOLT-LMM pipeline

BOLT-LMM specifications

Information


Unique identifier OMICS_13504
Name BOLT-LMM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data High-confidence set of SNPs, imputed SNPs, phenotypes, covariates, missing data treatment, genotype QC, user-specified filters
Input format PLINK, BED, BIM, FAM, DOSAGE, IMPUTE2, BGEN, FAM
Output data Association statistics in a tab-delimited file
Operating system Unix/Linux
Computer skills Advanced
Version 2.3.2
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Po-Ru Loh <>

Publication for BOLT-LMM

BOLT-LMM IN pipelines

 (2)
2017
PMCID: 5619771
PMID: 28957414
DOI: 10.1371/journal.pone.0185083

[…] the microarrays for variants on the x (n = 19,381) and y (n = 284) chromosomes, and on the mitochondrial genome (n = 135), which were unavailable in the imputed dataset., gwas was performed using bolt-lmm, a software that uses linear mixed-effect models to determine associations between each variant and the outcome, incorporating genetic relatedness [33]. we provided all directly genotyped […]

2017
PMCID: 5619771
PMID: 28957414
DOI: 10.1371/journal.pone.0185083

[…] models to determine associations between each variant and the outcome, incorporating genetic relatedness [33]. we provided all directly genotyped snps that were present in the imputed data to bolt-lmm to construct the model. for x, y and mitochondrial variants we used plink (v1.9) [37] to determine the associations between genotype and phenotype, with additional adjustment for the first 5 […]

BOLT-LMM institution(s)
Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA; Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA; Department of Endocrinology, Children’s Hospital Boston, Boston, MA, USA; Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
BOLT-LMM funding source(s)
Supported by NIH grant R01 HG006399 and NIH fellowship F32 HG007805; by the Fannie and John Hertz Foundation; by HL043851 and HL080467 from the National Heart, Lung, and Blood Institute and CA047988 from the National Cancer Institute, the Donald W. Reynolds Foundation and the Fondation Leducq, with collaborative scientific support and funding for genotyping provided by Amgen.

BOLT-LMM reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review BOLT-LMM