bam_impute_stitch

Subworkflow to impute BAM files using STITCH software. Variants location to impute are obtain through the legend 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.

BAMimputationstitch

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

Description

Input

name

description

pattern

`ch_input`

Channel with input data

`ch_posfile`

Channel with position to call variants by chromosomes

`ch_chunks`

Channel with chromosome chunks data

`ch_map`

Channel with genetic map data

`ch_fasta`

Channel with reference genome data

`k_val`

K value for STITCH imputation

`n_gen`

Number of generations for STITCH imputation

`buffer`

Buffer size around each chunk for STITCH imputation

`seed`

Random seed for STITCH imputation

Output