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.

step_config:
  hla_typing:
    #path_ngs_mapping: ../ngs_mapping
    #
    # Override data set configuration search paths for FASTQ files
    #path_link_in: ''
    #tools:                                            # Options: 'optitype', 'arcashla'
    #  - optitype
    #optitype:
    #
    #  # 5000 is a suggestion by OptiType author
    #  max_reads: 5000
    #  num_mapping_threads: 4
    #arcashla:
    #  mapper: star

Available HLA Typing Tools

The following HLA typing tools are currently available

  • "optitype"

  • "arcashla"