Running PharmCAT

This document teaches you how to use the core PharmCAT tool.

Prerequisites

Install the Software

You can skip this if are running PharmCAT in Docker.

You will need Java 17 or newer.
Download the PharmCAT Jar file from our releases page.

Prepare Your VCF Files

PharmCAT takes VCF files as input.

Please make sure you have read and understand PharmCAT's VCF requirements.

If you are not preparing your VCF files yourself, we highly recommend you run your VCF file through PharmCAT's VCF Preprocessor.

Running PharmCAT

This is the basic command, which will take your VCF file and produce the PharmCAT report:

# java -jar <path_to_pharmcat_jar_file> -vcf <vcf_file>

Where:

-jar <path_to_jar_file>: The compiled PharmCAT Jar file
-vcf <vcf_file>: Input VCF file (must comply with PharmCAT's VCF requirements)

By default, the output will be saved to the same directory as the input VCF file and will use the same base file name. For example:

# java -jar pharmcat.jar -vcf /tmp/sample1.vcf
Saving named allele matcher JSON results to /tmp/sample1.match.json
Saving phenotyper JSON results to /tmp/sample1.phenotype.json
Saving reporter HTML results to /tmp/sample1.report.html

Notice that all intermediary files will be kept.

To control this behavior, provide:

-o <dir> or --output-dir <dir>: Directory to save files to
-bf <name> or --base-filename <name>: The base name (without file extensions) used for output files
-del or --delete-intermediary-files: Delete intermediary output files

Example:

# java -jar pharmcat.jar -vcf /tmp/input.vcf -o /tmp/results -bf sample
Saving named allele matcher JSON results to /tmp/results/sample.match.json
Saving phenotyper JSON results to /tmp/results/sample.phenotype.json
Saving reporter HTML results to /tmp/results/sample.report.html

# java -jar pharmcat.jar -vcf /tmp/input.vcf --output-dir /tmp/results -del
Saving reporter HTML results to /tmp/results/input.report.html

If the provided VCF file contains multiple samples, you can limit which samples get processed with either:

-S <txt_file> or --sample-file <txt_file>: The list of samples to be processed and prepared for PharmCAT. The file should contain one sample per line.
-s <samples> or --samples <samples>: A comma-separated list of sample IDs.

Outside Calls

If you need to provide diplotypes directly to PharmCAT, you can do so using an "outside calls" file. You might want to do this for genes that PharmCAT does not call directly, or to override PharmCAT's call.

To do so, provide:

-po <tsv_file> or --phenotyper-outside-call-file <tsv_file>: Path to an outside call file (TSV)

Example:

# java -jar pharmcat.jar -vcf /tmp/sample.vcf -po /tmp/outside_calls.tsv
Saving named allele matcher JSON results to /tmp/results/sample.match.json
Saving phenotyper JSON results to /tmp/results/sample.phenotype.json
Saving reporter HTML results to /tmp/results/sample.report.html

Advanced Usage

Remember that the PharmCAT tool is composed of 3 modules: the Named Allele Matcher, the Phenotyper, and the Reporter.

graph LR;
  MI{{vcf file}} --> M[Named Allele Matcher];
  M --> P[Phenotyper];
  PI{{"outside call file"}} -. optional .-> P;
  P --> R[Reporter];
  R --> RO([HTML report]);
  class M,P,R module;
  class PI optional;

Each module has its own arguments to customize its behavior.

Named Allele Matcher

-matcher: run Named Allele Matcher
-ma or --matcher-all-results: return all possible diplotypes, not just top hits
-matcherHtml or --matcher-save-html: save named allele matcher results as HTML

Phenotyper

-phenotyper: run Phenotyper
-pi <json_file> or --phenotyper-input <json_file>: JSON results from named allele matcher
-po <tsv_file> or --phenotyper-outside-call-file <tsv_file>: path to an outside call file (TSV)

Reporter

-reporter: run Reporter
-ri <json_file> or --reporter-input <json_file>: JSON results from phenotyper
-rt <title> or --reporter-title <title>: text to add to the report title
-rs <CPIC or DPWG> or --reporter-sources <CPIC or DPWG>: comma-separated list of sources to limit recommendations to (defaults to both)
-re or --reporter-extended: generate extended report (includes all possible genes and drugs, even if no data is available)
-reporterJson: save reporter results as JSON

Running Individual Modules

Just the `Named Allele Matcher`

This will call the diplotypes for the input VCF file.

Examples:

# java -jar pharmcat.jar -matcher -vcf /tmp/sample.vcf
Saving named allele matcher JSON results to /tmp/sample.match.json

Just the `Phenotyper`

This will take matcher and/or call data and output function and phenotype information for them.

Examples:

# java -jar pharmcat.jar -phenotyper -pi /tmp/sample1.match.json
Saving phenotyper JSON results to /tmp/results/sample1.phenotype.json

# java -jar pharmcat.jar -phenotyper -pi /tmp/sample2.match.json -po /tmp/outside_calls.tsv
Saving phenotyper JSON results to /tmp/results/sample2.phenotype.json

# java -jar pharmcat.jar -phenotyper -po /tmp/outside_calls.tsv
Saving phenotyper JSON results to /tmp/results/outside_calls.phenotype.json

Just the `Reporter`

This will take the phenotyper data and output the relevant drug annotations in a comprehensive HTML report.

Examples:

# java -jar pharmcat.jar -reporter -ri /tmp/sample1.phenotype.json
Saving reporter HTML results to /tmp/results/sample1.report.html

# java -jar pharmcat.jar -reporter -ri /tmp/sample2.phenotype.json -rt "Awesome Report" -reporterJson
Saving reporter JSON results to /tmp/results/sample1.report.json
Saving reporter HTML results to /tmp/results/sample1.report.html

Combinations

Run Named Allele Matcher and Phenotyper:

# java -jar pharmcat.jar -matcher -vcf /tmp/sample1.vcf -phenotyper
Saving named allele matcher JSON results to /tmp/sample1.match.json
Saving phenotyper JSON results to /tmp/results/sample1.phenotype.json

# java -jar pharmcat.jar -matcher -vcf /tmp/sample2.vcf -phenotyper -po /tmp/outside_calls.tsv
Saving named allele matcher JSON results to /tmp/sample2.match.json
Saving phenotyper JSON results to /tmp/results/sample2.phenotype.json

Run Phenotyper and Reporter:

# java -jar pharmcat.jar -phenotyper -pi /tmp/sample1.phenotype.json -po /tmp/outside_calls.tsv -reporter
Saving phenotyper JSON results to /tmp/results/sample1.phenotype.json
Saving reporter HTML results to /tmp/results/sample1.report.html

# java -jar pharmcat.jar -phenotyper -po /tmp/outside_calls.tsv -reporter
Saving phenotyper JSON results to /tmp/results/outside_calls.phenotype.json
Saving reporter HTML results to /tmp/results/outside_calls.report.html

Research-Only Options

PharmCAT has two options that enables functionality meant for research use only!

Calling combination and partial alleles

To call combinations and partial alleles, use the --research combinations flag.

For details on combinations and partial alleles, please see NamedAlleleMatcher 201.

Remember that this is intended for research use only.

If given the --research combinations flag, PharmCAT will try to call combination and partial alleles. These are only called if an exact match to any single defined allele cannot be found. Without this research flag these samples will yield a "not called" result from the Named Allele Matcher.

This option addresses variant combinations not catalogued by PharmVar or other nomenclature sites. It does not consider novel variants; it only considers variants included in existing allele definitions found in novel combinations.

A combination allele is when a sample matches a combination of 2 or more defined alleles. For example, [*6 + *14] in the CYP2B6 [*6 + *14]/*13 diplotype output.

PharmCAT’s syntax for combination calls uses square brackets to reflect that it is a variation on one gene copy and to distinguish it from gene duplications (e.g. tandem arrangements like CYP2D6 *36+*10).

A partial allele is when a sample matches all the (core) variants of a defined allele but also has additional variants. For example, CYP2C19 *2/[*17 + g.94781859G>A]. In the case where a partial call occurs off the reference allele, only the positions are listed (e.g. *2/g.94781859G>A). A partial off the reference allele will only be called if the data is phased, or the unphased data only has 2 possible sequence combinations.

Note that PharmCAT only provides the match(es) with the highest score by default. Because PharmCAT scores on the number of matched positions in the definitions, the reference named allele (usually *1) will get the highest score. As such, scoring is biased towards grouping combinations together. For example, CYP2B6 *1/[*5 + *9 + *23] will be the call with the highest score but permutations such as *5/[*9 + *23], *9/[*5 + *23], *23/[*5 + *9] are also valid.

Calling CYP2D6

For details on calling CYP2D6 in PharmCAT, see Calling CYP2D6.

This option is not listed here because we do NOT recommend calling CYP2D6 from VCF, and Calling CYP2D6 explains why and what your options are.

Custom Definition Files

Advanced users can provide PharmCAT with custom allele definitions:

-def <dir> or --definitions-dir <dir>: directory containing named allele definitions (JSON files)

This can be used to get PharmCAT to call diplotypes for genes that PharmCAT does not support by default. Unless these are genes that PharmCAT supports through outside calls, PharmCAT will NOT be able to match them to any recommendations.

Running PharmCAT

Prerequisites

Install the Software

Prepare Your VCF Files

Running PharmCAT

Outside Calls

Advanced Usage

Named Allele Matcher

Phenotyper

Reporter

Running Individual Modules

Just the Named Allele Matcher

Just the Phenotyper

Just the Reporter

Combinations

Research-Only Options

Calling combination and partial alleles

Calling CYP2D6

Custom Definition Files

Just the `Named Allele Matcher`

Just the `Phenotyper`

Just the `Reporter`