Description

This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM file

*.{bam,cram}

input_index (file)

BAM/CRAM index file

*.{bai,crai}

fasta (file)

Reference file the CRAM file was created with (required with CRAM input)

*.{fasta,fa}

fasta_fai (file)

Index of the reference file (optional, but recommended)

*.{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

bigWig (file)

BigWig file

*.bigWig

bedgraph (file)

Bedgraph file

*.bedgraph
included in
nascent sammyseq
maintainers
Github user FriederikeHanssen
Github user SusiJo
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

deeptools
GPL v3

A set of user-friendly tools for normalization and visualzation of deep-sequencing data

deeptools.readthedocs.io/en/develop/content/tools/bamCoverage https://github.com/deeptools/deepTools/ 10.1093/nar/gkw257