Somatic Variant Expression

Implementation of the somatic_variant_expression step

This step allows the combination of somatic variant calling results with their expression from RNA-seq data. This allows for (1) extending a somatic VCF file with columns for the corresponding RNA-seq data giving depth of coverage and minor allele fraction in the tumor RNA-eq and (2) for computing a p value for likelihood of observation by chance.

Note

Status: not implemented yet

Step Input

Note

TODO

Step Output

Note

TODO

Default Configuration

The default configuration is as follows.

step_config:
  somatic_variant_expression:
    path_ngs_mapping: ../ngs_mapping                          # REQUIRED
    path_somatic_variant_calling: ../somatic_variant_calling  # REQUIRED