Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

Output

name:type
description
pattern

covstats{:bash}

meta{:bash}

:map

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

*.stats.txt{:bash}

:file

Coverage statistics

*.stats.txt

hist{:bash}

meta{:bash}

:map

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

*.hist.txt{:bash}

:file

Histogram of # occurrences of each depth level

*.hist.txt

versions_bbmap{:bash}

${task.process}{:bash}

:string

The name of the process

bbmap{:bash}

:string

The name of the tool

bbversion.sh | grep -v 'Duplicate cpuset'{:bash}

:eval

The expression to obtain the version of the tool

versions_samtools{:bash}

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools version | sed '1!d;s/.* //'{:bash}

:eval

The expression to obtain the version of the tool

versions_pigz{:bash}

${task.process}{:bash}

:string

The name of the process

pigz{:bash}

:string

The name of the tool

pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

bbmap{:bash}

:string

The name of the tool

bbversion.sh | grep -v 'Duplicate cpuset'{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools version | sed '1!d;s/.* //'{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

pigz{:bash}

:string

The name of the tool

pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//"{:bash}

:eval

The expression to obtain the version of the tool

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/software-tools/bbtools/bb-tools-user-guide https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh
included in
nascent
maintainer
Github user edmundmiller
get in touch
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