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

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).

2.184                                              March 2016                                         FastQTL(1)

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.

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

Name

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

Options

Basicoptions--help
              Print help about options.

       --silent
              Silent mode on terminal.

       --seed arg (=1459232241)
              Random number generator seed.  Useful to replicate runs of the software.

   InputandOutputfilesoptions-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.

   ExclusionandInclusionfilesoptions--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.