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)

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