NAME

       vcf-phased-join - take multiple overlapping pre-phased chunks and concatenates them into one VCF

SYNOPSIS

       vcf-phased-join [OPTIONS] A.vcf B.vcf C.vcf

DESCRIPTION

       About: The script takes multiple overlapping pre-phased chunks and concatenates them into one VCF

              using heterozygous calls from the overlaps to determine correct phase.

OPTIONS

       -j, --min-join-quality <num>
              Quality threshold for gluing the pre-phased blocks together [10]

       -l, --list <file>
              List of VCFs to join.

       -o, --output <file>
              Output file name. When "-" is supplied, STDOUT and STDERR will be used

       -q, --min-PQ <num>
              Break pre-phased segments if PQ value is lower in input VCFs [0.6]

       -h, -?, --help
              This help message

vcf-phased-join                                   February 2013                               VCF-PHASED-JOIN(1)