FastQTL protocols

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FastQTL specifications

Information


Unique identifier OMICS_10934
Name FastQTL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Version 2-184
Stability Stable
Maintained Yes

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Publication for FastQTL

FastQTL in pipeline

2017
PMCID: 5316867
PMID: 28195176
DOI: 10.1038/ncomms14418

[…] were used in normalization. the cis region was defined as ±1 mb from the transcription start site for each gene. the associations between genotypes and gene quantification were obtained using the fastqtl software., a reduced genome was generated by extracting the sequences flanking the nlaiii restriction sites (30 bp on each strand from the nlaiii restriction sites to downstream) using […]


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FastQTL in publications

 (9)
PMCID: 5904163
PMID: 29666371
DOI: 10.1038/s41467-018-03554-9

[…] in the cis-eqtl data by the gtex consortium (n = 277) for subcutaneous adipose tissue, filtered using their permutation test for significance, which used the adaptive permutation scheme in fastqtl and a permutation test p-value threshold equal to the empirical p-value of the gene closest to the fdr 5% threshold, as reported by gtex. only replicated adipose cis-eqtls and their target […]

PMCID: 5824840
PMID: 29476079
DOI: 10.1038/s41467-018-03209-9

[…] probes, 423 604 methylation probes, and 8 639 940 genotyped and imputed snps. snp and probes separated by <500 kb were tested for associationbeta distribution-adjusted empirical p-values from fastqtl were used to calculate q-values and a false-discovery rate (fdr) threshold of 0.01 was applied to identify eprobes/mecpgs with a significant eqtl/meqtla counts include snps in high ldb […]

PMCID: 5696339
PMID: 29158497
DOI: 10.1038/s41467-017-01775-y

[…] none of the index snps were associated with the expression of their flanking genes, snps in weak ld with rs12302097 were found to be nominally associated with the expression of chst11 (rs56372209, p fastqtl = 0.041, r 2 = 0.3) and txnrd1 (rs73183724, p fastqtl = 0.031, r 2 = 0.25, supplementary data ). using gtex we also found that several snps in complete ld with rs410155 including rs381706 […]

PMCID: 5776756
PMID: 29022597
DOI: 10.1038/nature24277

[…] metrics. in addition, we have observed that little, if any, genetic signal is present in the peer factors ()., within each tissue, cis-eqtls were identified by linear regression, as implemented in fastqtl, adjusting for peer factors, sex, genotyping platform, and three genotype-based principal components (pcs). we restricted our search to variants within 1 mb of the tss of each gene and, […]

PMCID: 5609773
PMID: 28922377
DOI: 10.1371/journal.pcbi.1005766

[…] finally, nominal p-values pnom were transformed to permutation p-values by pperm = p(x > −log10(pnom)) where x ~ g(μ, β). this procedure is conceptually very similar to the one implemented in the fastqtl tool, where beta distribution is used to model the smallest non-transformed p-values []., second, to control for the number of genes tested, we used the bonferroni method. all snp and gene […]


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FastQTL institution(s)
Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland; Swiss Institute of Bioinformatics, Geneva, Switzerland; NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Norway
FastQTL funding source(s)
This research is supported by grants from European Commission SYSCOL FP7, European Research Council, Louis Jeantet Foundation, Swiss National Science Foundation, SystemsX, the NIHNIMH (GTEx) and Helse Sør Øst.

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