vcf_impute_glimpse

Subworkflow to impute VCF files using GLIMPSE V1 software. The subworkflow takes VCF files, phased reference panel, and genetic maps to perform imputation and outputs phased and imputed VCF files. Meta map of all channels, except ch_input, will be used to perform joint operations. “regionout”, “regionoutPadded”, “regionSize” keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used.

glimpsechunkphaseligate

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/vcf_impute_glimpse

Description

Input

name

description

pattern

`ch_vcf`

Channel with target VCF files

`ch_ref`

Channel with reference phased VCF files

`ch_chunks`

Channel with chunks data

`ch_map`

Channel with genetic map data (optional)

`chunk`

Whether to perform chunking of the input data before imputation.

Output

name

description

pattern

`chunks`

Tab delimited output txt file containing buffer and imputation regions.
Structure: [meta, txt]

`merged_variants`

Output phased VCF/BCF file for the merged regions.
Phased information (HS field) is updated accordingly for the full region.
Structure: [ val(meta), bcf ]

`merged_variants_index`

Index output of phased VCF/BCF file for the merged regions.
Structure: [ val(meta), csi ]