Provided by: fastqtl_2.184+dfsg-7build2_amd64 bug


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


       fastQTL [options]


       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
              Print help about options.

              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
              List of samples to exclude.

              List of samples to include.

              List of sites to exclude.

              List of sites to include.

              List of phenotypes to exclude.

              List of phenotypes to include.

              List of covariates to exclude.

              List of covariates to include.

              To perform quantile normalization on the phenotype  quantifications  to  make  them
              normally  distributed.   Implemented  as  the  rntransform  function of the GenABEL

       -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.

       -P, --permute
              Permutation pass to calculate corrected p-values for molecular phenotypes.

              Permutation sequence.

       --map  Map best QTL candidates per molecular phenotype.

              Scan full cis-window to discover independent signals.

              Test for interactions with variable specified in file.

       -K, --chunk
              Specify which chunk needs to be processed.

              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
       zcat results.*.txt.gz | gzip -c > fastqtl_expected_output.txt.gz



       FastQTL  was  written  by  Olivier  Delaneau,  Halit  Ongen,  Alfonso  Buil  and   Manolis

       This manual page was written by Dylan Aïssi <>, for the Debian project
       (but may be used by others).