github.com/Breast-Oncology-Computational-Group/public-workflows/Gene_CN_Uniform_Category

Automatic Tools and Workflows
1

Workflow description

Gene_CN_Uniform_Category

This workflow processes gene copy number (CN) annotation files to create a uniform categorization of copy number variants.

Input

  • gene_cn_annotation_file: A TSV file containing gene copy number annotations with columns including sample, gene, LOH, CNAP, AMP_Classification, Loss_Classification, DeepDeletion, Variant_Classification, and Variant_Type.

Process

  1. Reads the input TSV file
  2. Standardizes variant classifications by:
This is a companion discussion topic for the original entry at github.com/Breast-Oncology-Computational-Group/public-workflows/Gene_CN_Uniform_Category