.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.41.1.
.TH VCF-CONTRAST "1" "February 2013" "vcf-contrast" "User Commands"
.SH NAME
vcf-contrast \- finds differences amongst samples
.SH SYNOPSIS
.B vcf-contrast
\fI+<list> -<list> \fR[\fIOPTIONS\fR] \fIfile.vcf.gz\fR
.SH DESCRIPTION
About: Finds differences amongst samples adding NOVEL* annotation to INFO field.
.SH OPTIONS
.TP
+<list>
List of samples where unique variant is expected
.TP
\-<list>
List of background samples
.TP
\fB\-d\fR, \fB\-\-min\-DP\fR <int>
Minimum depth across all \-<list> samples
.TP
\fB\-f\fR, \fB\-\-apply\-filters\fR
Skip sites with FILTER column different from PASS or "."
.TP
\fB\-n\fR, \fB\-\-novel\-sites\fR
Print only records with novel genotypes
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message.
.SS "Example:"
.IP
# Test if any of the samples A,B is different from all C,D,E
vcf\-contrast +A,B \fB\-C\fR,D,E \fB\-m\fR file.vcf.gz
.IP
# Same as above but printing only sites with novel variants and table output
vcf\-contrast \fB\-n\fR +A,B \fB\-C\fR,D,E \fB\-m\fR file.vcf.gz | vcf\-query \fB\-f\fR '%CHROM %POS\et%INFO/NOVELTY\et%INFO/NOVELAL\et%INFO/NOVELGT[\et%SAMPLE %GTR %PL]\en'
.IP
# Similar to above but require minimum mapping quality of 20
vcf\-annotate \fB\-f\fR MinMQ=20 file.vcf.gz | vcf\-contrast +A,B,C \fB\-D\fR,E,F \fB\-f\fR
.IP