Description

Calculates genome-wide sequencing coverage.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

Input BAM/CRAM file

*.{bam,cram}

bai (file)

Index for BAM/CRAM file

*.{bai,crai}

bed (file)

BED file with intersected intervals

*.{bed}

meta2 (map)

Groovy Map containing bed information
e.g. [ id:‘test’ ]

fasta (file)

Reference genome FASTA file

*.{fa,fasta}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

global_txt (file)

Text file with global cumulative coverage distribution

*.{global.dist.txt}

regions_txt (file)

Text file with region cumulative coverage distribution

*.{region.dist.txt}

summary_txt (file)

Text file with summary mean depths per chromosome and regions

*.{summary.txt}

per_base_bed (file)

BED file with per-base coverage

*.{per-base.bed.gz}

per_base_csi (file)

Index file for BED file with per-base coverage

*.{per-base.bed.gz.csi}

per_base_d4 (file)

D4 file with per-base coverage

*.{per-base.d4}

regions_bed (file)

BED file with per-region coverage

*.{regions.bed.gz}

regions_csi (file)

Index file for BED file with per-region coverage

*.{regions.bed.gz.csi}

quantized_bed (file)

BED file with binned coverage

*.{quantized.bed.gz}

quantized_csi (file)

Index file for BED file with binned coverage

*.{quantized.bed.gz.csi}

thresholds_bed (file)

BED file with the number of bases in each region that are covered at or above each threshold

*.{thresholds.bed.gz}

thresholds_csi (file)

Index file for BED file with threshold coverage

*.{thresholds.bed.gz.csi}

versions (file)

File containing software versions

versions.yml

Tools

mosdepth
MIT

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.