vcf-phased-join1
Take multiple overlapping pre-phased chunks and concatenates them into one vcf
Usage
vcf-phased-join [OPTIONS]
A.vcf
B.vcf
C.vcf
Overview
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]
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-l, --list <file> -
List of VCFs to join.
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-o, --output <file> -
Output file name. When "-" is supplied, STDOUT and STDERR will be used
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-q, --min-PQ <num> -
Break pre-phased segments if PQ value is lower in input VCFs [0.6]
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-h, -?, --help -
This help message
Releases
Unchanged in 6 releases since Debian 8 (Jessie).