kcotto/optitype repository overview

usage: OptiType [-h] --input FQ [FQ ...] (--rna | --dna) [--beta B]
                [--enumerate N] --outdir OUTDIR [--prefix PREFIX] [--verbose]
                [--config CONFIG]

OptiType: 4-digit HLA typer

optional arguments:
  -h, --help            show this help message and exit
  --input FQ [FQ ...], -i FQ [FQ ...]
                        .fastq file(s) (fished or raw) or .bam files stored
                        for re-use, generated by an earlier OptiType run. One
                        file: single-end mode, two files: paired-end mode.
  --rna, -r             Use with RNA sequencing data.
  --dna, -d             Use with DNA sequencing data.
  --beta B, -b B        The beta value for for homozygosity detection (see
                        paper). Default: 0.009. Handle with care.
  --enumerate N, -e N   Number of enumerations. OptiType will output the
                        optimal solution and the top N-1 suboptimal solutions
                        in the results CSV. Default: 1
  --outdir OUTDIR, -o OUTDIR
                        Specifies the out directory to which all files should
                        be written.
  --prefix PREFIX, -p PREFIX
                        Specifies prefix of output files
  --verbose, -v         Set verbose mode on.
  --config CONFIG, -c CONFIG
                        Path to config file. Default: config.ini in the same
                        directory as this script