Identifies low coverage in selected genomic regions (e.g. genes) based on mosdepth-like coverage info (e.g. genome wide coverage annotation).
LowCover can be installed from GitHub within R if you have BiocManager and remotes installed
> # install.packages("BiocManager")
> # install.packages("remotes")
> BiodManager::install("Jefferys/LowCover")LowCover is an R package with a "CLI" wrapper function. This allows it to be used from within R, run from a local script, or executed within a container.
LowCover uses the future package for parallel processing. Most users who know nothing about the future package will just want to set the option --parallel guess; this makes LowCover run with (all available) cores using a forking process where that is supported or with one R session per core where not. Without this parameter or additional environmental setup, LowCover runs purely sequentially. If you know something about future, e.g. you want to use your own custom future::plan() to manage running R code, LowCover will let you; it will use whatever plan already exists when it runs, or in the normal way use the R options that future defines to choose a default. It also tries to be friendly if you do choose to use the --parallel option, restoring any pre-existing future plan contexts when it exits.
The main function LowCoverApp() is designed to be called from a script, as it automatically loads the R script command line parameters internally and parses them. However, it can be run in an R session by passing command line options and values as a vector, e.g.:
LowCoverApp( c( "--targetsFile", "targets.bed",
"--coverageFile", "mozdepth.coverage.gz",
"--parallel", "guess" ))Create a script (or copy it from the Docker directory)
LowCover
!/usr/bin/env Rscript
LowCover::LowCoverApp()Running this is done from the shell command line like a normal program, generally passing --targetsFile, --coverageFile, and --parallel.
$ LowCover --targetFile "targets.bed" --coverageFile "mozdepth.coverage.gz" \
--parallel "guess"You can copy this script somewhere on your path to make it globally available.
You can use a pre-existing docker container or build you own
docker login quay.io
docker pull `quay.io/unclineberger/jefferys/lowcover:latest`Assumes you have docker, and that the contents of the Docker directory from the LowCover repository is available locally.
cd Docker
docker build -t <local name>:<tag> .This builds a container named <local name>:<tag>, e.g. lowcover:latest
Running involves simply running LowCover in the Docker container. For example
docker run -it --rm -v `pwd`:`pwd`, -w `pwd` LowCover \
--targetFile "targets.bed" \
--coverageFile "mozdepth.coverage.gz" \
--parallel "guess"To run with singularity, convert to a singularity file and run that. You can either pull to a sif directly from quay.io
singularity login quay.io
singlualrity pull docker://quay.io/unclineberger/jefferys/lowcover:latest <local name>:<tag>or convert a local container with
singlualrity pull docker-daemon://quay.io/unclineberger/jefferys/lowcover:latest <local name>:<tag>The sif will be named <local name>_<tag>.sif
Then run it with singularity
singularity run --B `pwd`:`pwd`, --pwd `pwd` LowCover \
--targetFile "targets.bed" \
--coverageFile "mozdepth.coverage.gz" \
--parallel "guess"Help is available, e.g. from the shell with
LowCover --helpor from R with
LowCover::LowCoverApp( "--help" )
Which currently returns
usage: LowCover [--] [--help] [--version] [--force] [--targetsFile TARGETSFILE]
[--coverageFile COVERAGEFILE] [--keep KEEP] [--chrY CHRY] [--regionsFile
REGIONSFILE] [--badGenesFile BADGENESFILE] [--goodGenesFile GOODGENESFILE]
[--summaryFile SUMMARYFILE] [--summaryFileNoY SUMMARYFILENOY] [--parallel
PARALLEL] [--workers WORKERS]
Low coverage reporting
Reports low coverage genomic regions based on mosdepth.
flags:
-h, --help show this help message and exit
-V, --version Print version info to stderr and exit.
-f, --force Create any non-existing directories and overwrite any
existing files.
optional arguments:
-t, --targetsFile Bed4 file of target regions to limit coverage reporting
to (column #4 = gene name), gzipped ok. [default:
targets.bed]
-c, --coverageFile Bed4 file reporting regions and their coverage class
(column #4 = coverage tag), gzipped ok. [default:
coverage.bed]
-k, --keep Comma separated string of tags identifying low coverage
regions. [default: NO_COVERAGE,LOW_COVERAGE]
-y, --chrY Name of 'Y' chromosome, if want to filter by sex.
[default: NA]
-r, --regionsFile Bed4 file of regions with low coverage (column #4 = gene
name). [default: LowCover.regions.bed]
-b, --badGenesFile Text file listing genes with at least 1 base with low
coverage (one per line). [default: LowCover.badgenes.txt]
-g, --goodGenesFile Text file listing genes with no low covage (one per
line). [default: LowCover.goodgenes.txt]
-s, --summaryFile Stats table as a tab-delimited file. [default:
LowCover.summary.tsv]
-S, --summaryFileNoY Stats table ignoring chrY. Only if --chrY is set.
[default: LowCover.summaryNoY.tsv]
-p, --parallel How to parallelize. Uses the 'future' R package. One of
'default', 'guess', 'multicore', 'multisession', or
'sequential' where: 'default' = Uses the plan set before
running LowCover, or as defined by the R options used by
`future`. 'guess' = Chooses 'multicore' if supported,
otherwise choose 'multisession'. 'multicore' = Fork
separately to each core/worker. May not not be supported.
'multisession' = One R session per core/worker.
'sequential' = Do not run in parallel; uses just one
core/worker. [default: default]
-w, --workers In parallel mode, set this to limit workers/cpus. By
default all available cpus as determined by
future::availableCores() are used. Note: this is ignored
if --parallel is either unset, 'default', or
'sequential'.
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