bam_impute_quilt2

Impute low-coverage BAM or CRAM inputs with QUILT2 and ligate chunked outputs per chromosome. “regionout”, “regionoutPadded”, “regionSize” keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used.

bamcramimputationquiltquilt2vcf

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_impute_quilt2

Description

Input

name

description

pattern

`ch_input`

Channel with target sequencing data and optional rename files.

`ch_reference_panel`

Channel with phased reference panel VCFs per chromosome.

`ch_chunks`

Channel with optional imputation chunks per chromosome.

`ch_map`

Channel with optional genetic maps per chromosome.

`ch_fasta`

Channel with optional reference FASTA data, required for CRAM inputs.

`n_gen`

Number of generations since founding or mixing.

`buffer`

Buffer of region to perform imputation over.

Output