Computes the depth at each position or region.
meta1:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
meta2:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
intervals:file
list of positions or regions in specified bed file
*.{bed}
tsv
*.tsv:file
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
versions.yml:file
File containing software versions
versions.yml
Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region
