Somatic Variant Checking

Implementation of the germline somatic_variant_checking step

The somatic_variant_checking step takes as the input the results of the somatic_variant_annotation step. It then executes various tools computing statistics on the result files and consistency checks with the pedigrees.

Note

Status: not implemented yet

Step Input

The variant calling step uses Snakemake sub workflows for using the result of the somatic_variant_annotation step.

Step Output

Note

TODO

Global Configuration

Note

TODO

Default Configuration

The default configuration is as follows.

step_config:
  somatic_variant_checking:
    path_somatic_variant_calling: ../somatic_variant_calling  # REQUIRED

Reports

Currently, no reports are generated.