mosdepth/mosdepth

coverage

depth

mosdepth

bam

cram

Description

Fast calculation of BAM/CRAM depth-of-coverage, producing per-base depth,
windowed/region coverage, quantized coverage, and threshold summaries from
a coordinate-sorted, indexed alignment file.

Inputs

Name	Type & Properties	Description
--input	file required	Coordinate-sorted BAM or CRAM file to calculate depth for.
--input_index	file	Index for `--input` (`.bai` for BAM, `.crai` for CRAM). If not provided, an index is expected alongside the input file.
--fasta -f	file	Reference FASTA file. Required when `--input` is a CRAM file.
--fasta_index	file	FASTA index (`.fai`) for `--fasta`. If not provided, an index is expected alongside the FASTA file.

Name

Type & Properties

--input

file

required

--input_index

file

--fasta

-f

file

--fasta_index

file

Outputs

Name	Type & Properties	Description
--output_summary	file output	Summary of mean depth per chromosome and genome-wide.
--output_global_dist	file output	Cumulative distribution of proportion of bases covered at or above each depth, genome-wide and per chromosome.
--output_region_dist	file output	Same as `--output_global_dist`, but for selected regions. Only produced when `--by_window`/`--by_bed` is set.
--output_per_base	file output	Per-base depth. Not produced if `--no_per_base` is set.
--output_per_base_index	file output	CSI index of `--output_per_base`.
--output_regions	file output	Mean (or median, see `--use_median`) depth per region. Only produced when `--by_window`/`--by_bed` is set.
--output_regions_index	file output	CSI index of `--output_regions`.
--output_quantized	file output	Quantized coverage regions. Only produced when `--quantize` is set.
--output_quantized_index	file output	CSI index of `--output_quantized`.
--output_thresholds	file output	Number of bases covered at or above each of `--thresholds` per region. Only produced when `--thresholds` is set, which in turn requires `--by_window`/`--by_bed` to also be set.
--output_thresholds_index	file output	CSI index of `--output_thresholds`.

Name

Type & Properties

--output_summary

file

output

--output_global_dist

file

output

--output_region_dist

file

output

--output_per_base

file

output

--output_per_base_index

file

output

--output_regions

file

output

--output_regions_index

file

output

--output_quantized

file

output

--output_quantized_index

file

output

--output_thresholds

file

output

--output_thresholds_index

file

output

Coverage Options

Name	Type & Properties	Description
--by_window	integer	Restrict `--output_regions`/`--output_region_dist` output to windows of this fixed size. Cannot be used with `--by_bed`.
--by_bed	file	Restrict `--output_regions`/`--output_region_dist` output to the intervals in a BED file. Cannot be used with `--by_window`.
--quantize -q	string	Colon-separated list of coverage cutoffs to quantize `--output_quantized` into. `N` cutoffs produce `N - 1` bins between consecutive cutoffs. Add a trailing colon (e.g. `0:1:5:100:500:`) to also get a final open-ended bin from the last cutoff to infinity.
--quantize_labels	string multiple	Custom labels for the `--quantize` bins, replacing their default numeric range labels in `--output_quantized`. The number of labels must match the number of bins produced by `--quantize`.
--thresholds -T	integer multiple	Coverage thresholds to report per region in `--output_thresholds`. Requires `--by_bed`/`--by_window` to be set.
--use_median -m	boolean_true	Output the median depth of each region in `--output_regions` instead of the mean. Only has an effect when `--by_window`/`--by_bed` is set.
--no_per_base -n	boolean_true	Don't output per-base depth. Speeds up execution substantially. Prefer `--quantize` or `--thresholds` if possible.
--fast_mode -x	boolean_true	Don't look at internal CIGAR operations or correct mate overlaps. Recommended for most use-cases.
--fragment_mode -a	boolean_true	Count the coverage of the full fragment, including the insert (proper pairs only).
--dist_precision	integer	Number of decimal places to report in `--output_global_dist`/ `--output_region_dist`. Default: 2.

Name

Type & Properties

--by_window

integer

--by_bed

file

--quantize

-q

string

--quantize_labels

string

multiple

--thresholds

-T

integer

multiple

--use_median

-m

boolean_true

--no_per_base

-n

boolean_true

--fast_mode

-x

boolean_true

--fragment_mode

-a

boolean_true

--dist_precision

integer

Read Filtering

Name	Type & Properties	Description
--mapq -Q	integer	Mapping quality threshold. Reads with a lower quality are ignored. Default: 0.
--flag -F	integer	Exclude reads with any of these SAM flag bits set. Default: 1796.
--include_flag -i	integer	Only include reads with any of these SAM flag bits set (0 is unset). Default: 0.
--min_frag_len -l	integer	Minimum insert size. Reads with a smaller insert size are ignored (-1 is unset). Default: -1.
--max_frag_len -u	integer	Maximum insert size. Reads with a larger insert size are ignored (-1 is unset). Default: -1.
--chrom -c	string	Restrict depth calculation to this chromosome.
--read_groups -R	string multiple	Read group IDs to restrict depth calculation to.

Name

Type & Properties

--mapq

-Q

integer

--flag

-F

integer

--include_flag

-i

integer

--min_frag_len

-l

integer

--max_frag_len

-u

integer

--chrom

-c

string

--read_groups

-R

string

multiple

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output_summary: "$id.$key.output_summary.txt"  
output_global_dist: "$id.$key.output_global_dist.txt"  
output_region_dist: "$id.$key.output_region_dist.txt"  
output_per_base: "$id.$key.output_per_base.gz"  
output_per_base_index: "$id.$key.output_per_base_index.csi"  
output_regions: "$id.$key.output_regions.gz"  
output_regions_index: "$id.$key.output_regions_index.csi"  
output_quantized: "$id.$key.output_quantized.gz"  
output_quantized_index: "$id.$key.output_quantized_index.csi"  
output_thresholds: "$id.$key.output_thresholds.gz"  
output_thresholds_index: "$id.$key.output_thresholds_index.csi"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.5.0 \  
  -main-script target/nextflow/mosdepth/mosdepth/main.nf \  
  -params-file params.yaml

mosdepth/mosdepth

Inputs

Outputs

Coverage Options

Read Filtering

Run this component

Relationships

Used by

Uses