.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.41.1.
.TH VCF-PHASED-JOIN "1" "February 2013" "vcf-phased-join" "User Commands"
.SH NAME
vcf-phased-join \- take multiple overlapping pre\-phased chunks and concatenates them into one VCF
.SH SYNOPSIS
.B vcf-phased-join
[\fIOPTIONS\fR] \fIA.vcf B.vcf C.vcf\fR
.SH DESCRIPTION
About: The script takes multiple overlapping pre\-phased chunks and concatenates them into one VCF
.IP
using heterozygous calls from the overlaps to determine correct phase.
.SH OPTIONS
.TP
\fB\-j\fR, \fB\-\-min\-join\-quality\fR <num>
Quality threshold for gluing the pre\-phased blocks together [10]
.TP
\fB\-l\fR, \fB\-\-list\fR <file>
List of VCFs to join.
.TP
\fB\-o\fR, \fB\-\-output\fR <file>
Output file name. When "\-" is supplied, STDOUT and STDERR will be used
.TP
\fB\-q\fR, \fB\-\-min\-PQ\fR <num>
Break pre\-phased segments if PQ value is lower in input VCFs [0.6]
.TP
\fB\-h\fR, \-?, \fB\-\-help\fR
This help message
.IP