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).