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pharmcat
William Rowell edited this page Jan 10, 2025
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2 revisions
flowchart TD
phased_vcf[/"phased small variant VCF"/] --> preprocess["pharmcat preprocess"]
aBAM[/"haplotagged BAM"/] --> filter["filter preprocessed VCF"]
preprocess --> filter
filter --> pharmcat["PharmCat"]
pharmcat --> outputs[/"PharmCat outputs"/]
PharmCat (Pharmacogenomics Clinical Annotation Tool) analyzes genetic variants and predicts drug response. In this subworkflow implementation, PharmCat will use a combination of the small variant VCF and pbStarPhase outupts. PharmCat outputs will only be generated if the depth at the variant position is greater than pharmcat_min_coverage (default 10). If no variants pass this filter, no outputs will be generated.
Citation: K Sangkuhl & M Whirl-Carrillo, et al. Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clinical Pharmacology & Therapeutics (2020) 107(1):203-210. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977333.