Computes the depth at each position or region.
meta1
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
index
BAM/CRAM index file
*.{bai,crai}
meta2
Groovy Map containing sample information e.g. [ id:‘test’ ]
intervals
list of positions or regions in specified bed file
*.{bed}
tsv
*.tsv
The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position
*.{tsv}
versions_samtools
${task.process}
:string
The process the versions were collected from
samtools
The tool name
samtools version | sed "1!d;s/.* //"
:eval
The expression to obtain the version of the tool
versions
Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region
