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

:map

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

input

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

index

:file

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

*.{bai,crai,csi}

intervals

:file

Interval FILE. Optional.

*.bed

meta2

:map

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

fasta

:file

FASTA reference file. Optional.

*.{fasta,fa,fna}

fai

:file

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

*.{fai}

Output

name:type
description
pattern

mpileup

meta

:map

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

*.mpileup.gz

:file

mpileup file

*.{mpileup}

versions_samtools

${task.process}

:string

The process the versions were collected from

samtools

:string

The tool name

samtools version | sed '1!d;s/.* //'

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The process the versions were collected from

samtools

:string

The tool name

samtools version | sed '1!d;s/.* //'

: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
Github user matthdsm
get in touch
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