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.