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fgwas specifications


Unique identifier OMICS_11295
Name fgwas
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.3.6
Stability Stable
GNU Scientific, Boost
Maintained Yes


No version available



  • person_outline Joseph Pickrell

Publication for fgwas

fgwas citations


Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

PMCID: 5828664
PMID: 29412141
DOI: 10.7554/eLife.31977.047

[…] ) consortium were used to compare the ability of the 450 k, 850 k and WGBS methylation array to interrogate T2D and FG GWAS regions.The DIAGRAM and ENGAGE GWAS SNP summary level data was used for the FGWAS analysis to determine enrichment of regulatory annotations in T2D and FG GWAS signal.Furthermore, data from () and () were used to categories T2D GWAS loci into physiological groups of insulin s […]


Rare non coding variants are associated with plasma lipid traits in a founder population

Sci Rep
PMCID: 5704019
PMID: 29180722
DOI: 10.1038/s41598-017-16550-8

[…] sex as adding kinship as a random effect to correct for the relatedness between the individuals in our sample. Causal variants were then prioritized based on functional annotations as implemented in fgwas. Follow-up conditional analyses were carried out in GEMMA for 6,781,373 variants in the Hutterites called in at least 400 individuals and with MAF > 1%. […]


Leveraging genome characteristics to improve gene discovery for putamen subcortical brain structure

Sci Rep
PMCID: 5691156
PMID: 29147026
DOI: 10.1038/s41598-017-15705-x

[…] Applying fgwas to our putamen GWAS summary statistics data, only one SNP was prominent at posterior probability > 0.5, two SNPs (in the same LD block) at posterior probability > 0.4, nine SNPs (in four LD bloc […]


Genomewide association study identifies a novel locus for cannabis dependence

Mol Psychiatry
PMCID: 5938138
PMID: 29112194
DOI: 10.1038/mp.2017.200

[…] informed consent and protocols were approved by the institutional review boards overseeing the individual studies (see ).Summary statistics from European ancestry subjects in CATS, COGA-ccGWAS, COGA-fGWAS, OZALC+ and SAGE were combined to form the discovery analysis. Replication analyses were conducted in the Yale-Penn () sample which was the major dataset contributing to the prior study by Sherv […]


Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations

Nat Commun
PMCID: 5559603
PMID: 28814792
DOI: 10.1038/s41467-017-00366-1

[…] We used the fgwas software to investigate the extent to which reQTLs and ceQTLs were enriched within specific annotation categories. Annotation information used by fgwas was derived from CADD variant consequence […]


Single trait and multi trait genome wide association analyses identify novel loci for blood pressure in African ancestry populations

PLoS Genet
PMCID: 5446189
PMID: 28498854
DOI: 10.1371/journal.pgen.1006728
call_split See protocol

[…] entified variants in r2>0.1 with the index variant and calculated causal evidence (Bayes Factors) for each variant. We then tested for enrichment in the causal evidence of variants in DHS sites using fGWAS.[] We found enrichment of blood/immune DHS (Enrichment = 3.1) and cardiovascular DHS (blood vessel Enrichment = 28.7, heart Enrichment = 2.0), in addition to DHS in several fetal tissues (). Can […]


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fgwas institution(s)
New York Genome Center, New York, NY, USA; Department of Biological Sciences, Columbia University, New York, NY, USA

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