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:false ]

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

bigwig

meta:map

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

*.bigWig:file

BigWig file

*.bigWig

bedgraph

meta:map

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

*.bedgraph:file

Bedgraph file

*.bedgraph

versions

versions.yml:file

File containing software versions

versions.yml

Tools

deeptools
GPL v3

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

deeptools.readthedocs.io/en/develop/content/tools/bamCoverage https://github.com/deeptools/deepTools/ 10.1093/nar/gkw257
included in
nascent sammyseq
maintainers
Github user FriederikeHanssen
Github user SusiJo
Github user JoseEspinosa
get in touch
Ask a question on Slack Open an issue on GitHub