fastQTL(1)

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.