vcf-phased-join(1)
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
-