pharmcat-runner 0.0.16

Installs, runs, and parsers PharmCAT using Pharmacoscan input.

PharmCAT Runner

The PharmCAT Runner tool provides a simplified pipeline for installing, running, and parsing PharmCAT outputs.

Dependencies

1. bcftools/tabix/bgzip - 1.18+
2. PLINK - Required for Hardy Weinburg and sample call rate QC methods
3. Python 3.9+ - Optional but highly recommended

Installation

Installation can be acheived using pip or any other package manager of your choosing. It is highly recommended that installation is done with Python 3.9+. Some conda environments can conflict with installation of a new verison.

pip install pharmcat_runner 

Usage

# Install PharmCAT and all required dependencies. If an installation already exists, must pass --overwrite to update
python3 -m pharmcat_runner install

# Standardize VCFs
python3 -m pharmcat_runner standardize --files "data/*.vcf"

# Run optional QC steps followed by PharmCAT
python3 -m pharmcat_runner haplotype --files "data/*.vcf" --hwe 0.001 --variant_call_rate 0.95 --sample_call_rate 0.95

# Parse PharmCAT output
# Original Pharmacoscan VCFs are required for accurate reporting of CYP2D6 copy number
# Sex ids are required for accurate reporting of G6PD
# Warnings are reported if either of these are not supplied
python3 -m pharmcat_runner parser --files "results/pharmcat_output/*.json" --vcfs "data/*.vcf" --sex_ids sex_ids.txt

sex_ids file

This file is required for accurate reporting of G6PD genotypes and phenotypes. This should be a tab delimited file without a header. The two columns should be sample id and predicted sex (M-Male, F-Female, O-Other). The sample ids in this file must match the sample ids in the pharmcat output

1234	M
5678	F
1357	O

Bugs and desired features

Please report any bugs and/or desired features to either the github issues page or to [e-mail]