NAME

       QTLtools extract - Data extraction mode.

SYNOPSIS

       QTLtools extract [--vcf --bed --cov] relevant_file --out output_prefix [OPTIONS]

DESCRIPTION

       Extract  all  the  data from the provided files into one flat file.  This will also impute
       all the missing data.

OPTIONS

       --vcf [in.vcf|in.bcf|in.vcf.gz]
              Genotypes in VCF/BCF format.  At least one of --vcf --bed --cov is REQUIRED.

       --bed quantifications.bed.gz
              Molecular phenotype quantifications in BED format.  At least  one  of  --vcf  --bed
              --cov is REQUIRED.

       --cov covariates.txt
              Covariates data.  At least one of --vcf --bed --cov is REQUIRED.

       --out filename_prefix
              Output file name prefix.  REQUIRED.

       --region chr:start-end
              Genomic region to be processed.  E.g. chr4:12334456-16334456, or chr5.

OUTPUT FILES

       .content.txt.gz
        Flat file with samples in rows and all the extracted variables in columns.

       .header.txt
        Genomic locations of the extracted variables.

EXAMPLE

       o Extract genotypes, gene quantifications, and covariates from a certain region:

         QTLtools  extract  --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov
         genes.covariates.pc50.txt.gz --region chr22:17000000-18000000 --out extract_output

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)