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(),
  bascet_instance = GetDefaultBascetInstance()
)

Arguments

outputName

Name of output file (BIGWIG-file)