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}

meta3:map

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

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

versions.yml:file

File containing software versions

versions.yml

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.