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