vcf_impute_glimpse

Impute VCF/BCF files with Glimpse

glimpsechunkphaseligate

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

Description

Impute VCF/BCF files with Glimpse

Input

name:type

description

pattern

`ch_input :file`

Target dataset in VCF/BCF format defined at all variable positions.
Index file of the input VCF/BCF file containing genotype likelihoods.
File with sample names and ploidy information.
Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
Reference panel of haplotypes in VCF/BCF format.
Index file of the Reference panel file.
File containing the genetic map.
The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
Structure: [ meta, vcf, csi, txt, region, ref_vcf, ref_csi, gmap ]

Output

name:type

description

pattern

`chunk_chr :file`

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

`merged_variants :file`

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 :file`

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

`versions :file`

File containing software versions

versions.yml