From aligned BAM file, compute counts per chromosome
Usage
BascetCountChrom(
bascetRoot,
inputName = "aligned",
outputName = "chromcount",
minMatching = 0,
removeDuplicates = TRUE,
overwrite = FALSE,
runner = GetDefaultBascetRunner(),
bascetInstance = GetDefaultBascetInstance()
)Arguments
- bascetRoot
The root folder where all Bascets are stored
- inputName
Name of input shard
- outputName
Name of output shard
- minMatching
Disregard reads having fewer than specified matches, based on CIGAR string
- removeDuplicates
Deduplicate reads
- 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