Description

Determines the depth in a BAM/CRAM file

Input

Name (Type)
Description
Pattern

meta (map)

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

]

meta2 (map)

Groovy Map containing information for the fasta
e.g. [ id:‘test’, single_end

]

meta3 (map)

Groovy Map containing information for the fasta_fai
e.g. [ id:‘test’, single_end

]

input (file)

BAM/CRAM file

*.{bam,cram}

input_index (file)

Index of the BAM/CRAM file

*.{bai,crai}

fasta (file)

Reference genome FASTA

*.{fasta,fna,fa}

fasta_fai (file)

Index of the reference genome FASTA

*.fai

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

depth (file)

A JSON file containing depth, depth variance, read length and other parameters

*.json

binned_depth (file)

A TSV file containing the binned normalized depth. Can only be calculated for CRAM files

*.tsv

Tools

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Apache License 2.0

Graph realignment tools for structural variants