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
]
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
]
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
]
*.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.
