bam_impute_quilt

Subworkflow to impute BAM files using QUILT software. Variants location to impute are obtain through the tsv file given. “regionout”, “regionoutPadded”, “regionSize” keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used.

BAMimputationquilt

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

Description

Input

name

description

pattern

`ch_input`

Channel with input data

`ch_hap_legend`

Channel with reference panel variants data

`ch_chunks`

Channel with chromosome chunks data

`ch_map`

Channel with genetic map data

`ch_fasta`

Channel with reference genome data

`n_gen`

Number of generations since founding or mixing

`buffer`

Buffer of region to perform imputation over

Output