Command-line Arguments

The inputs on this page reflect the parameters that are applicable for the command-line tool. To see the inputs required for tbp-parser when run as part of the TheiaProk workflow series, please refer to the TheiaProk Inputs page.

Required Inputs

tbp-parser is designed to run immediately after Jody Phelan’s TBProfiler tool. Only three inputs are required: the JSON file produced by TBProfiler and the BAM and BAI file produced by TBProfiler.

The JSON file contains information about the mutations detected in the sample: the quality, the type, and if that mutation confers resistance to an antimicrobial drug. The BAM file contains the alignment information for the sample and is needed for determining sequencing quality.

Parameter	Description
input_json	The path to the JSON file that was produced by TBProfiler
input_bam	The path to the BAM file that was produced by TBProfiler

BAM index file required

The BAM file must have the accompanying BAI file in the same directory. It must also be named exactly the same as the BAM file but ending with a .bai suffix.

Optional Inputs

tbp-parser can be customized with a number of optional input parameters. These parameters can be used to control the quality control thresholds, the text that appears in the reports, and the names of the output files. The following is a list of all the input parameters that can be used with tbp-parser.

In addition to these arguments, tbp-parser also has a -h, --help argument that will out the list of possible arguments and their descriptions and a -v, --version argument that will print out the version of tbp-parser that is installed. Both of these commands exit the program after printing their output.

Configuration File

Instead of providing the input parameters on the command line, the ability to provide a configuration file in YAML format is available. The configuration file will overwrite all command-line arguments, except for the --verbose and --debug arguments. The configuration file can be provided using the --config argument.

The configuration file can also be used to overwrite the global variables that are in use. The global variables available can be found in the Global Variables page.

To overwriite a variable, please use the following format in the configuration file. The variable names are case-sensitive.

# this variable is found in the globals.py file
GENES_FOR_LIMS:
  - "rpoB"
  - "inhA"
  - "pncA"
  - "inhA"

# although this variable can be set with an input parameter, it must be in uppercase here as it appears in the globals.py file
MIN_DEPTH: 15

# these command-line input parameters are not found in the globals.py file so they are indicated in lowercase
add_cs_lims: True
output_prefix: "Test"
coverage_regions: "/path/to/file"

# only variables that can be found in either globals.py or in the command-line arguments will be used
extra_variable: "This will be ignored"

Quality Control Arguments

These options determine the thresholds for quality control.

Short Version	Long Version	Description	Default Value
-d	--min_depth	The minimum depth of coverage required for a site to pass QC	10
-c	--min_percent_coverage	The minimum percentage of a region that has depth above the threshold set by min_depth (used for a gene/locus to pass QC)	100
-s	--min_read_support	The minimum read support for a mutation to pass QC	10
-f	--min_frequency	The minimum frequency for a mutation to pass QC (0.1 -> 10%)	0.1
-r	--coverage_regions	A BED file containing the regions to calculate percent coverage for	/data/tbdb-modified-regions.md

Text Arguments

These options are used verbatim in the reports, or are used to name the output files.

Short Version	Long Version	Description	Default Value
-m	--sequencing_method	The sequencing method used to gerneate the data; used in the LIMS & Looker reports. Enclose in quotes if including a space	"Sequencing method not provided"
-p	--operator	The operator who ran the analysis; used in the LIMS & Looker reports. Enclose in quotes if including a space	"Operator not provided"
-o	--output_prefix	The prefix to use for the output files. Do not include any spaces	"tbp-parser"

LIMS Arguments

These options are used to customize the LIMS report

Name	Description	Default Value
--add_cs_lims	Adds Cycloserine (CS) fields to the LIMS report	false

tNGS-specific Arguments

These options are primarily used for tNGS data, although all frequency and read support arguments are compatible with WGS data.

Name	Description	Default Value
--tngs	Indicates that the input data was generated using the Deeplex + CDPH modified protocol. Turns on tNGS-specific global parameters	false
--tngs_expert_regions	A BED file containing the regions to calculate coverage for expert rule regions. This is used to determine coverage quality in the regions where resistance-conferring mutations are found, or where a CDC expert rule is applied. This is not used for QC purposes	/data/tbdb-expert-regions.bed
--rrs_frequency	The minimum frequency for an rrs mutation to pass QC, as rrs has several problematic sites in the Deeplex tNGS assay	0.1
--rrl_frequency	The minimum frequency for an rrl mutation to pass QC, as rrl has several problematic sites in the Deeplex tNGS assay	0.1
--rrs_read_support	The minimum read support for an rrs mutation to pass QC, as rrs has several problematic sites in the Deeplex tNGS assay	10
--rrl_read_support	The minimum read support for an rrl mutation to pass QC, as rrl has several problematic sites in the Deeplex tNGS assay	10
--rpob449_frequency	The minimum frequency for an rpoB mutation at protein position 449 to pass QC, as this site is problematic in the Deeplex tNGS assay	0.1
--etha237_frequency	The minimum frequency for an ethA mutation at protein position 237 to pass QC, as this site is problematic in the Deeplex tNGS assay	0.1

Logging Arguments

These options change the verbosity of the stdout log

Name	Description	Default Value
--verbose	Increases the output verbosity to describe which stage of the analysis is currently running	false
--debug	The highest level of output verbosity detailing every step of the analysis and logic implemented; overwrites --verbose	false