Description

Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

stats (file)

Per-scaffold coverage info

*.stats.txt

hist (file)

Histogram of # occurrences of each depth level

*.hist.txt

versions (file)

File containing software versions

versions.yml
included in
nascent
author
Github user Emiller88
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Tools

bbmap
UC-LBL license (see package)

BBMap is a short read aligner, as well as various other bioinformatic tools.

jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh