NAME

       QTLtools rep - Replicate QTL associations in an independent dataset

SYNOPSIS

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

DESCRIPTION

       This mode reads phenotype-genotype pairs that  were  identified  in  another  dataset  and
       checks association between the same genotype and phenotype in this dataset.

OPTIONS

       --vcf [in.vcf|in.bcf|in.vcf.gz|in.bed.gz] ...
              Genotypes  in  VCF/BCF  format,  or  another molecular phenotype in BED format.  If
              there is a DS field in the genotype FORMAT of a variant  (dosage  of  the  genotype
              calculated  from  genotype probabilities, e.g. after imputation), then this is used
              as the genotype.  If there is only the GT field in the genotype FORMAT then this is
              used and it is converted to a dosage.  REQUIRED.

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

       --qtl external_qtls.txt ...
              The  file  listing  the  QTLs  identified  in  the external dataset.  One phenotype
              genotype pair (separated by space, phenotype first) per line.  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 phenotype's chromosome
         3   The phenotype's start position
         4   The phenotype's end position
         5   The phenotype's strand
         6   The genotype ID
         7   The genotype's chromosome
         8   The genotype's start position
         9   The genotype's end position
        10   The p-value of the association
        11   The slope of the association

EXAMPLE

       o Replicate  the  results  of  dataset1  in dataset2, correcting dataset2 phenotype's with
         technical covariates and normal transforming them:

         QTLtools rep --bed  dataset2.bed.gz  --vcf  dataset2.bcf  --cov  dataset2.covariates.txt
         --qtl significant_qtls_dataset1.txt --normal --out rep_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)