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

covstats

meta:map

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

]

*.stats.txt:file

Coverage statistics

*.stats.txt

hist

meta:map

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

]

*.hist.txt:file

Histogram of # occurrences of each depth level

*.hist.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

bbmap
UC-LBL license (see package)

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