NAME

       QTLtools gwas - Genome-wide association tests

SYNOPSIS

       QTLtools gwas --vcf [in.vcf|in.vcf.gz|in.bcf|in.bed.gz] --bed quantifications.bed.gz --out
       output.txt [OPTIONS]

DESCRIPTION

       This mode runs a linear regression with every genotype vs. every phenotype.

OPTIONS

       --vcf [in.vcf|in.bcf|in.vcf.gz|in.bed.gz] ...
              Genotypes in VCF/BCF/BED format.  The DS field in the genotype FORMAT of a  variant
              (dosage  of  the  genotype  calculated  from  genotype  probabilities,  e.g.  after
              imputation) is REQUIRED.  REQUIRED.

       --bed quantifications.bed.gz ...
              Molecular phenotype quantifications in BED format.  REQUIRED.

       --out filename.txt
              The output file name.  REQUIRED.

       --cov covariates.txt
              Covariates to correct the phenotype data with.

       --normal
              Rank normal transform the  phenotype  data  so  that  each  phenotype  is  normally
              distributed.  RECOMMENDED.

OUTPUT FILE

       output file
        Space separated output file with the following columns.

        1     The phenotype ID
        2     The variant's chromosome
        3     The variants's start position
        3.1   The variant's end position.  Only printed if a BED file is supplied to --vcf
        4     The variant's ID
        5     The p-value
        6     The correlation coefficient

EXAMPLE

       o Run  the  association between all the variants and phenotypes, correcting the phenotypes
         with technical covariates and normal transforming them:

         QTLtools gwas --bed  quantifications.bed.gz  --vcf  genotypes.bcf  --cov  covariates.txt
         --normal --out gwas_results.txt

SEE ALSO

       QTLtools(1)

       QTLtools website: <https://qtltools.github.io/qtltools>

BUGS

       Versions  up  to  and  including  1.2,  suffer  from a bug in reading missing genotypes in
       VCF/BCF files.  This bug affects variants with a DS field in their genotype's  FORMAT  and
       have a missing genotype (DS field is .) in one of the samples, in which case genotypes for
       all the samples are set to missing, effectively removing this variant from the analyses.

       Please submit bugs to <https://github.com/qtltools/qtltools>

CITATION

       Delaneau O., Ongen H., Brown A. A., et al. A complete tool set for molecular QTL discovery
       and analysis. Nat Commun 8, 15452 (2017).  <https://doi.org/10.1038/ncomms15452>

AUTHORS

       Olivier Delaneau (olivier.delaneau@gmail.com), Halit Ongen (halitongen@gmail.com)