Align from FASTQ, generate sorted and indexed BAM file

Align from FASTQ, generate sorted and indexed BAM file

Usage

BascetAlignToReference(
  bascetRoot,
  useReference,
  numLocalThreads = NULL,
  inputName = "asfq",
  outputNameBAMunsorted = "unsorted_aligned",
  outputNameBAMsorted = "aligned",
  doSort = TRUE,
  overwrite = FALSE,
  aligner = c(NULL, "BWA", "STAR"),
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored

useReference

Name of the BWA reference to use

numLocalThreads

Number of threads to use for each runner. Default is the maximum, taken from runner settings

inputName

Name of input shard

outputNameBAMunsorted

Name of unsorted BAMs

outputNameBAMsorted

Name of sorted BAMs (if generated)

doSort

Whether to sort the output or not

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