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:type

description

pattern

`meta :map`

Groovy Map containing sample information

`bam :file`

BAM or CRAM file

*.{bam,cram}

`bai :file`

BAM/SAM samtools index

*.{bai,csi}

`hapmap_file :file`

Hapmap file

Output

name:type

description

pattern

`meta :map`

Groovy Map containing sample information

`txt :file`

Contamination estimation file

*.txt

`versions :file`

File containing software versions

versions.yml