0.3.3

Mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

mosdepth can output:

• per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.

• mean per-window depth given a window size--as would be used for CNV calling.

• the mean per-region given a BED file of regions.

• the mean or median per-region cumulative coverage histogram given a window size

• a distribution of proportion of bases covered at or above a given threshold for each chromosome and genome-wide.

• quantized output that merges adjacent bases as long as they fall in the same coverage bins e.g. (10-20)

• threshold output to indicate how many bases in each region are covered at the given thresholds.

• A summary of mean depths per chromosome and within specified regions per chromosome.

CWL for running Mosdepth - Coverage tool

Version of tools in docker image

Tool	Version	Location
mosdepth	0.3.3	https://hub.docker.com/r/brentp/mosdepth/tags https://github.com/brentp/mosdepth/releases/tag/v0.3.3

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CWL

• CWL specification 1.0

• Use example_inputs.yaml to see the inputs to the cwl

• Example Command using toil:

    > toil-cwl-runner mosdepth_0.3.3.cwl example_inputs.yaml

#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/mosdepth_0.3.3.cwl /path/to/inputs.yaml

#Using toil-cwl-runner
> nohup toil-cwl-runner --singularity --outdir /path/to/output/folder /path/to/mosdepth_0.3.3.cwl /path/to/inputs.yaml &

Usage

usage: mosdepth_0.3.3.cwl [-h] [--memory_per_job MEMORY_PER_JOB]
                          [--memory_overhead MEMORY_OVERHEAD]
                          [--number_of_threads NUMBER_OF_THREADS] [--bed BED]
                          [--chrom CHROM] [--prefix PREFIX] [--flag FLAG]
                          [--mapq MAPQ]
                          [job_order]

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

positional arguments:
  job_order             Job input json file

optional arguments:
  -h, --help            show this help message and exit
  --memory_per_job MEMORY_PER_JOB
                        Memory per job in megabytes
  --memory_overhead MEMORY_OVERHEAD
                        Memory overhead per job in megabytes
  --number_of_threads NUMBER_OF_THREADS
  --bed BED             optional BED file or (integer) window-sizes.
  --chrom CHROM         chromosome to restrict depth calculation.
  --prefix PREFIX       Prefix for the output files
  --flag FLAG           exclude reads with any of the bits in FLAG set
  --mapq MAPQ           mapping quality threshold. reads with a mapping
                        quality less than this are ignored