multiple_impute_glimpse2

Impute VCF/BCF files, but also CRAM and BAM files with Glimpse2

glimpsechunkphaseligatesplit_reference

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/multiple_impute_glimpse2

Description

Impute VCF/BCF files, but also CRAM and BAM files with Glimpse2

Input

name:type

description

pattern

`ch_input :file`

Target dataset in CRAM, BAM or VCF/BCF format.
Index file of the input file.
File with sample names and ploidy information.
Structure: [ meta, file, index, txt ]

`ch_ref :file`

Reference panel of haplotypes in VCF/BCF format.
Index file of the Reference panel file.
Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
Structure: [ meta, vcf, csi, region ]

`ch_map :file`

File containing the genetic map.
Structure: [ meta, gmap ]

`ch_fasta :file`

Reference genome in fasta format.
Reference genome index in fai format
Structure: [ meta, fasta, fai ]

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 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 file of the ligated phased variants files.

`versions :file`

File containing software versions

versions.yml