NGS Sanity Checking

Implementation of the ngs_sanity_checking step

Perform sanity checking from mapped reads for germline sample sheets, optionally taking the result of hla_typing into consideration.

Note

Status: not implemented yet

Step Input

Note

TODO

Step Output

Note

TODO

Default Configuration

The default configuration is as follows.

# Default configuration ngs_sanity_checking
step_config:
  ngs_sanity_checking:
    path_ngs_mapping: ../path_ngs_mapping  # REQUIRED
    path_hla_typing: ../path_hla_typing    # OPTIONAl
    check_hla: true