produces a histogram or table of coverage per chromosome
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
input{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
input_index{:bash}
:file
BAM/CRAM index file
*.{bai,crai}
meta2{:bash}
:map
Groovy Map containing reference information
e.g. [ id:‘genome’ ]
fasta{:bash}
:file
Reference genome file
*.{fa,fasta}
fai{:bash}
:file
Reference genome index file
*.fai
Output
name:type
description
pattern
coverage{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.txt{:bash}
:file
Tabulated text containing the coverage at each position or region or an ASCII-art histogram (with —histogram).
*.txt
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
Topics
name:type
description
pattern
versions{: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
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.
