Description

produces a histogram or table of coverage per chromosome

Input

name:type
description
pattern

meta

:map

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

input

:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

input_index

:file

BAM/CRAM index file

*.{bai,crai}

meta2

:map

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

fasta

:file

Reference genome file

*.{fa,fasta}

fai

:file

Reference genome index file

*.fai

Output

name:type
description
pattern

coverage

meta

:map

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

*.txt

:file

Tabulated text containing the coverage at each position or region or an ASCII-art histogram (with —histogram).

*.txt

versions_samtools

${task.process}

:string

The name of the process

samtools

:string

The name of the tool

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

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

samtools

:string

The name of the tool

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

: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
abotyperphaseimpute
maintainers
Github user LouisLeNezet
Github user matthdsm
get in touch
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