.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.4.
.TH VCF-STATS "1" "July 2011" "vcf-stats 0.1.5" "User Commands"
.SH NAME
vcf-stats \- statistic of VCF file
.SH SYNOPSIS
.B vcf-stats
[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
.SH OPTIONS
.TP
\fB\-d\fR, \fB\-\-dump\fR <file>
Take an existing dump file and recreate the files (works with \fB\-p\fR)
.TP
\fB\-f\fR, \fB\-\-filters\fR <filter1,filter2>
List of filters such as column/field (any value), column/field=bin:max (cluster in bins),column/field=value (exact value)
.TP
\fB\-p\fR, \fB\-\-prefix\fR <dir/string>
Prefix of output files. If slashes are present, directories will be created.
.TP
\fB\-s\fR, \fB\-\-samples\fR <list>
Process only the listed samples, \- for none. Excluding unwanted samples may increase performance considerably.
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message.
.SH EXAMPLES
.IP
# Calculate stats separately for the filter field, quality and non\-indels
vcf\-stats file.vcf.gz \fB\-f\fR FILTER,QUAL=10:200,INFO/INDEL=False \fB\-p\fR out/
.IP
# Calculate stats for all samples
vcf\-stats file.vcf.gz \fB\-f\fR FORMAT/DP=10:200 \fB\-p\fR out/
.IP
# Calculate stats only for the sample NA00001
vcf\-stats file.vcf.gz \fB\-f\fR SAMPLE/NA00001/DP=1:200 \fB\-p\fR out/
.IP
vcf\-stats file.vcf.gz > perl.dump