debian man page for vcf-subset

VCF-SUBSET(1)							   User Commands						     VCF-SUBSET(1)

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

vcf-subset 0.1.5						     July 2011							     VCF-SUBSET(1)