Provided by: fastqtl_2.184+dfsg-6_amd64
FastQTL - Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
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.
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.
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
FastQTL was written by Olivier Delaneau, Halit Ongen, Alfonso Buil and Manolis Dermitzakis. This manual page was written by Dylan Aïssi <firstname.lastname@example.org>, for the Debian project (but may be used by others).