bam_docounts_contamination_angsd

Calculate contamination of the X-chromosome with ANGSD

angsdbamcontaminationdocounts

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

Description

Calculate contamination of the X-chromosome with ANGSD

Input

name

description

pattern

`ch_bam`

BAM/CRAM file and its index.

Structure: [ val(meta), path(bam), path(bai) ]

*.{bam,cram}

`ch_hapmap_file`

Hapmap file.

Structure: [ val(meta), path(hapmap_file) ]

Output

name

description

pattern

`txt`

Contamination estimation file.

Structure: [ val(meta), path(txt) ]

*.txt