A total of 88 samples were analyzed in this study, a subset of the 137 samples from the CDC Genetic Testing Reference Materials Coordination Program (GeT-RM) PGx study.
The reason for not using all samples for testing: sequencing data for other samples (either FASTQ or VCF) were not available from the published sources.
The test germline VCF files after tailoring based on the loci covered by PAnno are saved in the vcf directory, and the corresponding PAnno reports are saved in the report directory. In addition, the PAnno runs require information on the population to which each sample belongs, so an additional metadata is provided.
The raw VCF files were obtained from the 1000 Genomes Project, that were re-sequenced and analyzed by the New York Genome Center at 30x coverage (Byrska-Bishop et al., 2021) and are available at http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20190425_NYGC_GATK/raw_calls_updated/.