Description

Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

input_list{:bash}

:file

VCF/BCF files containing genotype probabilities (GP field). The files should be ordered by genomic position.

*.{vcf,bcf,vcf.gz,bcf.gz}

input_list_index{:bash}

:file

VCF/BCF files index.

*.csi

Output

name:type
description
pattern

merged_variants{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{vcf,bcf,vcf.gz,bcf.gz}{:bash}

:file

Output VCF/BCF file for the merged regions. Phased information (HS field) is updated accordingly for the full region.

*.{vcf,bcf,vcf.gz,bcf.gz}

versions_shapeit5{:bash}

${task.process}{:bash}

:string

The name of the process

shapeit5{:bash}

:string

The name of the tool

SHAPEIT5_ligate | sed "5!d;s/^.*Version *: //; s/ .*$//"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

shapeit5{:bash}

:string

The name of the tool

SHAPEIT5_ligate | sed "5!d;s/^.*Version *: //; s/ .*$//"{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
phaseimpute
maintainer
Github user louislenezet
get in touch
Ask a question on Slack Open an issue on GitHub