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)

QTLtools-v1.3                                      06 May 2020                                  QTLtools-gwas(1)