Description

Generate text pileup output for one or multiple BAM files. Each input file produces a separate group of pileup columns in the output.

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

index{:bash}

:file

CSI/BAI/CRAI file. Optional. Only required when using the ‘-r’ parameter.

*.{bai,crai,csi}

intervals{:bash}

:file

Interval FILE. Optional.

*.bed

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘test’ ]

fasta{:bash}

:file

FASTA reference file. Optional.

*.{fasta,fa,fna}

fai{:bash}

:file

FAI file. Optional. Only required (recommended) when using the ‘-f’ parameter.

*.{fai}

Output

name:type
description
pattern

mpileup{:bash}

meta{:bash}

:map

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

*.mpileup.gz{:bash}

:file

mpileup file

*.{mpileup}

versions_samtools{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

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

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

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

:string

The command used to generate the version of the tool

Tools

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352
included in
abotyperrnadnavarsarek
maintainers
Github user joseespinosa
Github user krannich479
get in touch
Ask a question on Slack Open an issue on GitHub