Align from FASTQ, generate sorted and indexed BAM file — BascetAlignToReference • Zorn

TODO Should be managed by Bascet mapshard system, with automatic input conversion. unaligned file should be made temp and removed

Usage

BascetAlignToReference(
  bascetRoot,
  useReference,
  numLocalThreads = 1,
  inputName = "asfq",
  outputNameBAMunsorted = "unsorted_aligned",
  outputNameBAMsorted = "aligned",
  do_sort = TRUE,
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascet_instance = GetDefaultBascetInstance()
)

Arguments

useReference: Name of the BWA reference to use
numLocalThreads: Number of threads to use for each runner
outputNameBAMunsorted: Name of unsorted BAMs
outputNameBAMsorted: Name of sorted BAMs (if generated)
do_sort: Whether to sort the output or not