Align from FASTQ, generate sorted and indexed BAM file

Align from FASTQ, generate sorted and indexed BAM file

Usage

BascetAlignToReference(
  bascetRoot,
  useReference,
  numThreads = NULL,
  totalMem = NULL,
  inputName = "filtered",
  outputName = "aligned",
  outputNameBAMcell = NULL,
  outputNameBAMpos = NULL,
  overwrite = FALSE,
  aligner = c(NULL, "BWAMEM2", "bowtie2", "STAR"),
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored

useReference

Name of the BWA reference to use

numThreads

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

totalMem

Total memory to allocate

inputName

Name of input shard

outputName

Output shard name prefix. Defaults to <outputName>_cell for the unsorted/cell BAM and <outputName>_pos for the position-sorted BAM.

outputNameBAMcell

Name of cell-sorted BAMs. If NULL, derived from outputName.

outputNameBAMpos

Name of pos-sorted BAMs. If NULL, derived from outputName.

overwrite

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

aligner

Which aligner to use: "BWAMEM2", "bowtie2", or "STAR"

runner

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

bascetInstance

A Bascet instance