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}

meta3 (map)

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

fasta (file)

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

*.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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

tsv (file)

An output TSV file containing the results of the gender prediction

*.tsv

Tools

ngsbits
MIT license

Short-read sequencing tools