Man page - vcf-phased-join(1)
Packages contas this manual
- vcf-subset(1)
- vcf-merge(1)
- vcf-compare(1)
- vcf-to-tab(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-contrast(1)
- vcf-isec(1)
- vcf-validator(1)
- fill-ref-md5(1)
- vcf-convert(1)
- vcf-annotate(1)
- vcf-concat(1)
- fill-an-ac(1)
- vcf-fix-newlines(1)
- vcf-query(1)
- vcf-stats(1)
- vcf-consensus(1)
- vcf-tstv(1)
- fill-aa(1)
- vcf-phased-join(1)
- fill-fs(1)
- vcf-shuffle-cols(1)
- vcftools(1)
- vcf-fix-ploidy(1)
Package: vcftools
apt-get install vcftools
apt-get install vcftools
Manuals in package:
Documentations in package:
Manual
| VCF-PHASED-JOIN(1) | User Commands | VCF-PHASED-JOIN(1) |
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
| February 2013 | vcf-phased-join |