NAME

       vcf-subset - create subset of VCF file

SYNOPSIS

       vcf-subset [OPTIONS] in.vcf.gz > out.vcf

OPTIONS

       -c, --columns <string>
              File  or  comma-separated  list  of  columns  to keep in the vcf file. If file, one
              column per row

       -e, --exclude-ref
              Exclude rows not containing variants.

       -p, --private
              Print only rows where only the subset columns carry an alternate allele.

       -r, --replace-with-ref
              Replace the excluded types with reference allele instead of dot.

       -t, --type <list>
              Comma-separated list of variant types to include: SNPs,indels.

       -u, --keep-uncalled
              Do not exclude rows without calls.

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

EXAMPLES

              cat in.vcf | vcf-subset -r -t indels -e -c SAMPLE1 > out.vcf