T cell CRG Report

Implementation of the tcell_crg_report step

This step collects all of the calls and information gathered for the BIH T cell CRG and generates an Excel report for each patient.

Note

Status: not implemented yet

Step Input

The BIH T cell CRG report generator uses the following as input:

somatic_variant_annotation
somatic_epitope_prediction
somatic_variant_checking
somatic_ngs_sanity_checks

Step Output

Note

TODO

Default Configuration

The default configuration is as follows.

# Default configuration tcell_crg_report
step_config:
  tcell_crg_report:
    path_somatic_variant_annotation: ../somatic_variant_annotation  # REQUIRED

Available Gene Fusion Callers

cnvkit