Understanding the Configuration YAML

Introduction

The steepest learning curve to utilizing Filtering Analysis Tool (FAT) is understanding how to turn filtering requirements into a corresponding configuration YAML.

Below is a fully-functional configuration YAML:

---
 output_file_name: 'Case_3_FL_FAT_02_25_21.xlsx'
 output_sheet_name: 'GTB12_Case_3_FL'
 stylesheet_choice: 'vaccine'
 full_protection: True
 filters:
   - filtering_type: 'BINARY'
     filtering_column: 'tumor_exome_day0_var_count'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_numeric_operator: '>='
       bfs_numeric_number: '5'
   - filtering_type: 'BINARY'
     filtering_column: 'normal_exome_day0_VAF'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_numeric_operator: '<='
       bfs_numeric_number: '4.99'
   - filtering_type: 'BINARY'
     filtering_column: 'FL_tumor_capture_alt'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_numeric_operator: '>='
       bfs_numeric_number: '4'
   - filtering_type: 'BINARY'
     filtering_column: 'tumor_exome_day0_ref_count_plus_tumor_exome_day0_var_count'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_numeric_operator: '>='
       bfs_numeric_number: '20'
   - filtering_type: 'BINARY'
     filtering_column: 'FL_tumor_capture_ref_plus_FL_tumor_capture_alt'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_numeric_operator: '>='
       bfs_numeric_number: '10'
   - filtering_type: 'BINARY'
     filtering_column: 'Capture_Val_Status'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_string_operator: '=='
       bfs_string_literal:
         - 'PASS'
   - filtering_type: 'BINARY'
     filtering_column: 'No_Capture_Coverage_Exome_Status'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_string_operator: '=='
       bfs_string_literal:
         - 'PASS'
   - filtering_type: 'BINARY'
     filtering_column: 'Call'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_string_operator: '=='
       bfs_string_literal:
         - 'S'
         - 'A'
   - filtering_type: 'BINARY'
     filtering_column: 'Consequence'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_string_operator: '=='
       bfs_string_literal:
         - 'NA'
         - 'frameshift_variant'
         - 'frameshift_variant,start_lost,start_retained_variant'
         - 'inframe_deletion'
         - 'missense_variant'
         - 'missense_variant,splice_region_variant'
         - 'splice_acceptor_variant'
         - 'splice_donor_variant'
         - 'splice_donor_variant,intron_variant'
         - 'splice_donor_variant,non_coding_transcript_variant'
         - 'splice_region_variant,intron_variant'
         - 'splice_region_variant,synonymous_variant'
         - 'start_lost'
         - 'stop_gained'
 add_filtering_status: True
 add_filtering_binaries: True
 ignore_binary_filtering_status:
   - 'FL_tumor_capture_alt'
   - 'FL_tumor_capture_ref_plus_FL_tumor_capture_alt'
   - 'Capture_Val_Status'