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FastQTL(1) General Commands Manual FastQTL(1)


FastQTL - Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes


fastQTL [options]


The goal of FastQTL is to identify single-nucleotide polymorphisms (SNPs) which are significantly associated with various molecular phenotypes (i.e. expression of known genes, cytosine methylation levels, etc). It performs scans for all possible phenotype-variant pairs in cis (i.e. variants located within a specific window around a phenotype). FastQTL implements a new permutation scheme (Beta approximation) to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels.


Basic options

Print help about options.
Silent mode on terminal.
Random number generator seed. Useful to replicate runs of the software.

Input and Output files options

Screen output is copied in this file.
Genotypes in VCF format.
Phenotypes in BED format.
Covariates in TXT format.
Phenotype groups in TXT format.
Output file.

Exclusion and Inclusion files options

List of samples to exclude.
List of samples to include.
List of sites to exclude.
List of sites to include.
List of phenotypes to exclude.
List of phenotypes to include.
List of covariates to exclude.
List of covariates to include.


To perform quantile normalization on the phenotype quantifications to make them normally distributed. Implemented as the rntransform function of the GenABEL package.

Cis-window size. Default values is 1Mb (1e6). It means that all variants within 1e6 bp of the phenotype location (e.g. TSS) is analyzed.
To filter out all phenotype-variant pairs with a p-value above the specified threshold in the output of a nominal pass.


Permutation pass to calculate corrected p-values for molecular phenotypes.
Permutation sequence.
Map best QTL candidates per molecular phenotype.
Scan full cis-window to discover independent signals.
Test for interactions with variable specified in file.


Specify which chunk needs to be processed.
Generates all commands.
Region of interest.


for c in $(seq 1 256); do
fastQTL --vcf genotypes.vcf.gz
--bed phenotypes.bed.gz
--chunk $c 256
--permute 1000
--out results.$c.txt.gz
zcat results.*.txt.gz | gzip -c > fastqtl_expected_output.txt.gz



FastQTL was written by Olivier Delaneau, Halit Ongen, Alfonso Buil and Manolis Dermitzakis.

This manual page was written by Dylan Aïssi <>, for the Debian project (but may be used by others).

March 2016 2.184