@article{Hari01012023,
author = {Hari, Ananth and Zhou, Qinghui and Gonzaludo, Nina and Harting, John and Scott, Stuart A. and Qin, Xiang and Scherer, Steve and Sahinalp, S. Cenk and Numanagić, Ibrahim}, 
title = {An efficient genotyper and star-allele caller for pharmacogenomics},
volume = {33}, 
number = {1}, 
pages = {61-70}, 
year = {2023}, 
doi = {10.1101/gr.277075.122}, 
abstract ={High-throughput sequencing provides sufficient means for determining genotypes of clinically important pharmacogenes that can be used to tailor medical decisions to individual patients. However, pharmacogene genotyping, also known as star-allele calling, is a challenging problem that requires accurate copy number calling, structural variation identification, variant calling, and phasing within each pharmacogene copy present in the sample. Here we introduce Aldy 4, a fast and efficient tool for genotyping pharmacogenes that uses combinatorial optimization for accurate star-allele calling across different sequencing technologies. Aldy 4 adds support for long reads and uses a novel phasing model and improved copy number and variant calling models. We compare Aldy 4 against the current state-of-the-art star-allele callers on a large and diverse set of samples and genes sequenced by various sequencing technologies, such as whole-genome and targeted Illumina sequencing, barcoded 10x Genomics, and Pacific Biosciences (PacBio) HiFi. We show that Aldy 4 is the most accurate star-allele caller with near-perfect accuracy in all evaluated contexts, and hope that Aldy remains an invaluable tool in the clinical toolbox even with the advent of long-read sequencing technologies.}, 
URL = {http://genome.cshlp.org/content/33/1/61.abstract}, 
eprint = {http://genome.cshlp.org/content/33/1/61.full.pdf+html}, 
journal = {Genome Research} 
}