Generate a bigwig out of all reads in a sorted BAM. Note that the caller is responsible for sorting the BAM first

This function is mainly for QC purposes. It uses bamCoverage from deepTools apt install python3-deeptools

Usage

BascetAlignmentToBigwig(
  bascetRoot,
  inputName = "aligned",
  outputName = "pileup",
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored

inputName

Name of input shard (BAM-file)

outputName

Name of output shard (BIGWIG-file)

overwrite

Force overwriting of existing files. The default is to do nothing files exist

runner

The job manager, specifying how the command will be run (e.g. locally, or via SLURM)

bascetInstance

A Bascet instance

Value

A runner job (details depends on runner)