Description

Determines the gender of a sample from the BAM/CRAM file.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

bam:file

One or more BAM/CRAM files to determine the gender of

*.{bam,cram}

bai:file

The index file(s) from the input BAM/CRAM file(s)

*.{bai,crai}

meta2:map

Groovy Map containing reference fasta information e.g. [ id:‘test’ ]

fasta:file

The reference FASTA to use (mandatory when CRAM files are used)

*.{fasta,fa,fna}

meta2:map

Groovy Map containing reference fasta information e.g. [ id:‘test’ ]

fai:file

The index file from the reference FASTA

*.fai

method:string

The method to use to define the gender (posibilities are ‘xy’, ‘hetx’ and ‘sry’)

(xy|hetx|sry)

Output

name:type
description
pattern

tsv

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.tsv:file

An output TSV file containing the results of the gender prediction

*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

ngsbits
MIT

Short-read sequencing tools