NAME

       vcf-query - query VCF files

SYNOPSIS

       query-vcf [OPTIONS] file.vcf.gz

OPTIONS

       -c, --columns <NA001,NA002,..>
              List of comma-separated column names.

       -f, --format <string>
              The default is '%CHROM:%POS\t%REF[\t%SAMPLE=%GT]\n'

       -l, --list-columns
              List columns.

       -r, --region chr:from-to
              Retrieve the region. (Runs tabix.)

       -h, -?, --help
              This help message.

EXAMPLES

              query-vcf  file.vcf.gz  1:1000-2000  -c  NA001,NA002,NA003 query-vcf file.vcf.gz -r
              1:1000-2000  -f  '%CHROM:%POS\t%REF[\t%SAMPLE:%*=,]\n'  query-vcf  file.vcf.gz   -f
              '[%GT\t]%LINE\n' query-vcf file.vcf.gz -f '%CHROM\t%POS\t%INFO/DP\t%FILTER\n'