Laboratorian report

The laboratorian report is the main report produced by tbp-parser and is used to generate all of the other reports. What follows is an explanation of all the columns in the report.

Any fields from TBProfiler are from the input JSON file produced by TBProfiler.

Column name	Explanation	Column source
sample_id	The name of the sample	TBProfiler "id" field
tbprofiler_gene_name	The name of the gene where the mutation has been identified	TBProfiler "gene_name" field
tbprofiler_locus_tag	The locus tag for the mutation that has been identified	TBProfiler "locus_tag" field OR by the gene database file indicated with the --gene_database_yml input parameter if the field is blank
tbprofiler_variant_substitution_type	The type of mutation identified, whether or not it was a frameshift, missense, or synonymous mutation	TBProfiler "type" field
tbprofiler_variant_substitution_nt	The mutation in nucleotide format	TBProfiler "nucleotide_change" field
tbprofiler_variant_substitution_aa	The mutation in amino acid format, if possible	TBProfiler "protein_change" field
genomic_start_pos	The genomic start position of the mutation	TBProfiler "pos" field
genomic_end_pos	The genomic end position of the mutation	Calculated from the TBProfiler "pos" field
confidence	Contains either: - the WHO annotation - an indication that there is no WHO annotation - NA for when there is no mutation	Edited by tbp-parser, originates from the TBProfiler "confidence" field
antimicrobial	The antimicrobial drug that may be affected by this mutation	TBProfiler "annotation.drug" field, split into multiple rows if multiple annotation items are present. May also originate from the "gene_associated_drugs" field if not all are included in the annotation
looker_interpretation	The drug resistance interpretation intended for the Looker report	Determined by tbp-parser
mdl_interpretation	The drug resistance interpretation intended for the LIMS report	Determined by tbp-parser
depth	The depth of coverage at the mutation	TBProfiler "depth" field
frequency	The frequency of the mutation in the reads	TBProfiler "freq" field
read_support	How many reads support the mutation (depth * frequency)	Calculated by tbp-parser
rationale	Contains an indication of what was used (the WHO annotation, the specific expert rule used, or neither) to create the two interpretations	Determined by tbp-parser
warning	Any potential quality warnings that may indicate lower reliability	Determined by tbp-parser
gene_tier	The gene tier of the mutation’s gene (Tier 1, Tier 2, or NA)	Determined by the gene database file indicated with the --gene_database_yml input parameter
source	The source of the mutation information (WHO v2 catalogue, tbdb, etc.)	TBProfiler "annotation.source" field
tbdb_comment	Any comments from TBProfiler about the mutation	TBProfiler "annotation.comment" field

Because of how a particular mutation may contribute resistance to different drugs at the same time, each mutation may be listed multiple times, once for each antimicrobial drug that could be impacted.

Any genes that do not have any mutations are also included in the laboratorian report with NA or WT in the appropriate field.

Customizing column names

To overwrite any of the output column names or text in the laboratorian report, please use the following format in a configuration file or use the command-line parameter --find_and_replace:

FIND_AND_REPLACE:
  "sample_id": "My_Sample_ID_Column"
  "tbprofiler_gene_name": "My_Gene_Name_Column"
  ...

Please note that this will rename every instance of that text in all output reports (every instance of "sample_id" will be renamed to "My_Sample_ID_Column" in all output files, etc.).