.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.4.
.TH VCF-QUERY "1" "July 2011" "vcf-query 0.1.5" "User Commands"
.SH NAME
vcf-query \- query VCF files
.SH SYNOPSIS
.B query-vcf
[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
.SH OPTIONS
.TP
\fB\-c\fR, \fB\-\-columns\fR <NA001,NA002,..>
List of comma\-separated column names.
.TP
\fB\-f\fR, \fB\-\-format\fR <string>
The default is '%CHROM:%POS\et%REF[\et%SAMPLE=%GT]\en'
.TP
\fB\-l\fR, \fB\-\-list\-columns\fR
List columns.
.TP
\fB\-r\fR, \fB\-\-region\fR chr:from\-to
Retrieve the region. (Runs tabix.)
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message.
.SH EXAMPLES
.IP
query\-vcf file.vcf.gz 1:1000\-2000 \fB\-c\fR NA001,NA002,NA003
query\-vcf file.vcf.gz \fB\-r\fR 1:1000\-2000 \fB\-f\fR '%CHROM:%POS\et%REF[\et%SAMPLE:%*=,]\en'
query\-vcf file.vcf.gz \fB\-f\fR '[%GT\et]%LINE\en'
query\-vcf file.vcf.gz \fB\-f\fR '%CHROM\et%POS\et%INFO/DP\et%FILTER\en'