SYNOPSIS

fastQTL [options]

DESCRIPTION

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.

OPTIONS

Basic options

--help

Print help about options.

--silent

Silent mode on terminal.

--seed arg (=1459232241)

Random number generator seed. Useful to replicate runs of the software.

Input and Output files options

-L, --log

Screen output is copied in this file.

-V, --vcf

Genotypes in VCF format.

-B, --bed

Phenotypes in BED format.

-C, --cov

Covariates in TXT format.

-G, --grp

Phenotype groups in TXT format.

-O, --out

Output file.

Exclusion and Inclusion files options

--exclude-samples

List of samples to exclude.

--include-samples

List of samples to include.

--exclude-sites

List of sites to exclude.

--include-sites

List of sites to include.

--exclude-phenotypes

List of phenotypes to exclude.

--include-phenotypes

List of phenotypes to include.

--exclude-covariates

List of covariates to exclude.

--include-covariates

List of covariates to include.

Parameters

--normal

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

-W, --window

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.

-T, --threshold

To filter out all phenotype-variant pairs with a p-value above the specified threshold in the output of a nominal pass.

Modes

-P, --permute

Permutation pass to calculate corrected p-values for molecular phenotypes.

--psequence

Permutation sequence.

--map

Map best QTL candidates per molecular phenotype.

--map-full

Scan full cis-window to discover independent signals.

--interaction

Test for interactions with variable specified in file.

Parallelization

-K, --chunk

Specify which chunk needs to be processed.

--commands

Generates all commands.

-R, --region

Region of interest.

EXAMPLE

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
done
zcat results.*.txt.gz | gzip -c > fastqtl_expected_output.txt.gz

AUTHOR

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

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