Man page - vcf-phased-join(1)
Packages contains this manual
- vcf-query(1)
- vcf-stats(1)
- vcf-to-tab(1)
- vcf-concat(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-phased-join(1)
- fill-aa(1)
- vcf-isec(1)
- vcf-consensus(1)
- vcf-tstv(1)
- vcf-merge(1)
- vcf-subset(1)
- vcf-contrast(1)
- vcf-fix-newlines(1)
- fill-an-ac(1)
- vcftools(1)
- vcf-validator(1)
- fill-fs(1)
- vcf-fix-ploidy(1)
- vcf-compare(1)
- fill-ref-md5(1)
- vcf-annotate(1)
- vcf-convert(1)
- vcf-shuffle-cols(1)
apt-get install vcftools
Manual
VCF-PHASED-JOIN
NAMESYNOPSIS
DESCRIPTION
OPTIONS
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