---
name: "fastQTL"
section: "1"
platform: "linux"
package: "fastqtl"
version: "2.184+v7+dfsg-4+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastQTL"
---

# fastQTL(1)

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

## 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).