---
name: "vcf-phased-join"
section: "1"
platform: "linux"
package: "vcftools"
version: "0.1.16-3+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcf-phased-join"
---

# vcf-phased-join(1)

take multiple overlapping pre-phased chunks and concatenates them into one VCF

## 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

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  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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