NAME

       QTLtools correct - Corrects genotypes or phenotypes with the provided covariates

SYNOPSIS

       QTLtools  correct --vcf [in.vcf|in.vcf.gz|in.bcf] | --bed in.bed.gz --cov covariates.txt |
       --normal --out output.txt [OPTIONS]

DESCRIPTION

       This mode corrects genotypes or phenotypes in VCF,  BCF,  or  BED  files  with  covariates
       provided and/or rank normal transforms the data and writes out the new corrected values to
       a file.  This mode regresses out the covariates from the data, and writes the residuals to
       a file.

OPTIONS

       --vcf [in.vcf|in.bcf|in.vcf.gz|in.bed.gz]
              Genotypes in VCF/BCF/BED format.  REQUIRED unless --bed.

       --bed quantifications.bed.gz
              Quantifications in BED format.  REQUIRED unless --vcf.

       --out output_file
              Output file name.  REQUIRED.

       --cov covariates.txt
              Covariates to correct the data with.  REQUIRED unless --normal.

       --qtl qtl_file [in.vcf|in.vcf.gz|in.bcf]
              Corrects  given  phenotypes  with  the  given genotypes.  Takes two arguments.  The
              first one is a text file listing genotype-phenotype pairs  (separated  by  a  space
              e.g.  snp1  gene1),  one  pair per line.  A phenotype will be corrected for all the
              genotypes provided  for  that  phenotype.   The  second  argument  is  a  VCF  file
              containing  the  genotypes.  The variant IDs in the qtl_file must match the variant
              IDs in the VCF file, and  the  phenotype  IDs  must  match  with  the  --bed  file.
              Requires --bed.

       --normal
              Rank normal transform the data.  REQUIRED unless --cov.

EXAMPLES

       o Correct  gene  quantifications  with  technical  covariates,  rank  normal transform the
         quantifications, and create a new bed file:

         QTLtools correct --bed quantifications.bed.gz --out quantifications_corrected.bed  --cov
         technical_covars.txt --normal

       o Correct the gene quantifications for eQTLs

         QTLtools  correct --bed quantifications.bed.gz --out quantifications_corrected.bed --qtl
         eQTL_variant_gene_pairs.txt

SEE ALSO

       QTLtools(1)

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

BUGS

       o 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. 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)