fastQTL1

Quantitative trait loci (qtl) mapper in cis for molecular phenotypes

Usage

fastQTL [options]

Overview

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.

Examples

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

Releases

Unchanged in 5 releases since Debian 9 (Stretch).

9–13