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}

intervals{:bash}

:file

Interval FILE

*.bed

meta2{:bash}

:map

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

fasta{:bash}

:file

FASTA reference file

*.{fasta,fa}

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

Name of the process

samtools{:bash}

:string

Name of the tool

samtools --version | head -1 | sed -e "s/samtools //"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

Name of the process

samtools{:bash}

:string

Name of the tool

samtools --version | head -1 | sed -e "s/samtools //"{:bash}

:eval

The expression to obtain 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
maintainer
Github user joseespinosa
get in touch
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