.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.4.
.TH VCF-SUBSET "1" "July 2011" "vcf-subset 0.1.5" "User Commands"
.SH NAME
vcf-subset \- create subset of VCF file
.SH SYNOPSIS
.B vcf-subset
[\fIOPTIONS\fR] \fIin.vcf.gz > out.vcf\fR
.SH OPTIONS
.TP
\fB\-c\fR, \fB\-\-columns\fR <string>
File or comma\-separated list of columns to keep in the vcf file. If file, one column per row
.TP
\fB\-e\fR, \fB\-\-exclude\-ref\fR
Exclude rows not containing variants.
.TP
\fB\-p\fR, \fB\-\-private\fR
Print only rows where only the subset columns carry an alternate allele.
.TP
\fB\-r\fR, \fB\-\-replace\-with\-ref\fR
Replace the excluded types with reference allele instead of dot.
.TP
\fB\-t\fR, \fB\-\-type\fR <list>
Comma\-separated list of variant types to include: SNPs,indels.
.TP
\fB\-u\fR, \fB\-\-keep\-uncalled\fR
Do not exclude rows without calls.
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message.
.SH EXAMPLES
.IP
cat in.vcf | vcf\-subset \fB\-r\fR \fB\-t\fR indels \fB\-e\fR \fB\-c\fR SAMPLE1 > out.vcf