vcf-query(1) debian man page | unix.com

VCF-QUERY(1)							   User Commands						      VCF-QUERY(1)

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	%REF[	%SAMPLE=%GT]
'

       -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	%REF[	%SAMPLE:%*=,]
'
	      query-vcf file.vcf.gz -f '[%GT	]%LINE
' query-vcf file.vcf.gz -f '%CHROM	%POS	%INFO/DP	%FILTER
'

vcf-query 0.1.5 						     July 2011							      VCF-QUERY(1)