This is the command vcf-phased-join that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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