HLA Typing

Implementation of the hla_typing step

The hla_typing step allows for the HLA typing from NGS read data (WGS, targeted DNA sequencing, or RNA-seq).

Step Input

Gene fusion calling starts at the raw RNA-seq reads. Thus, the input is very similar to one of ngs_mapping step.

See Step Input for more information.

Step Output

HLA typing will be performed for all NGS libraries in all sample sheets. For each combination of HLA typer and library, a directory {hla_typer}.{lib_name}-{lib_pk}/out will be created. Therein, the following files will be created:

• {hla_typer}.{lib_name}-{lib_pk}.txt

• {hla_typer}.{lib_name}-{lib_pk}.txt.md5

For example, it might look as follows for the example from above:

output/
+-- optitype.P001-N1-DNA1-WES1-4
|   `-- out
|       |-- optitype.P001-N1-DNA1-WES1-4.txt
|       `-- optitype.P001-N1-DNA1-WES1-4.txt.md5
[...]

Default Configuration

The default configuration is as follows.

# Default configuration ngs_mapping
step_config:
  hla_typing:
    path_ngs_mapping: ../ngs_mapping
    path_link_in: ""   # OPTIONAL Override data set configuration search paths for FASTQ files
    tools: [optitype]  # REQUIRED - available: 'optitype' and 'arcashla'
    optitype:
      max_reads: 5000  # suggestion by OptiType author
      num_mapping_threads: 4
    arcashla:
      mapper: star

Available HLA Typing Tools

The following HLA typing tools are currently available

• "optitype"

• "arcashla"