Take multiple overlapping pre-phased chunks and concatenates them into one vcf
vcf-phased-join [OPTIONS] A.vcf B.vcf C.vcf
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.
-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