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 |
CWL
CWL specification 1.0
Use example_inputs.yaml to see the inputs to the cwl
Example Command using toil:
Usage
Last updated