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

FastQTL(1) General Commands Manual FastQTL(1)

NAME

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

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
 
 

SEE ALSO

http://fastqtl.sourceforge.net/

AUTHOR

FastQTL was written by Olivier Delaneau, Halit Ongen, Alfonso Buil and Manolis Dermitzakis.
This manual page was written by Dylan Aïssi <bob.dybian@gmail.com>, for the Debian project (but may be used by others).
March 2016 2.184