OVERVIEW PacBio HiFi reads for pharmacogenomics reference samples from target enrichment Twist Alliance Long Read PGx Panel. 10 out of 24 samples sequenced on Sequel IIe SMRT Cell 8M are released here. METHODS SHEARING Covaris g-TUBE to target size of 8kb. TWIST LIBRARY Prepared according to https://www.twistbioscience.com/resources/protocol/long-read-library-preparation-and-standard-hyb-v2-enrichment Probes: Twist Alliance Long Read PGx Panel PACBIO LIBRARY Prepared according to https://www.pacb.com/wp-content/uploads/Procedure-checklist-Preparing-multiplexed-amplicon-libraries-using-SMRTbell-prep-kit-3.0.pdf SEQUENCING Sequel IIe System, 24 hr movie, Sequel II Chemistry 2.0, Binding Kit 3.2 ANALYSIS Generate HiFi reads with ccs v6.3.0 Demultiplex with lima v2.5.0 Mark PCR Duplicates with pbmarkdups v1.0.2 Align to GRCh38_no_alt_analysis_set with pbmm2 v1.7.0 Call variants with pbsv v2.8 and DeepVariant v1.4.0 Phase with whatshap 1.1 FILE DESCRIPTION bam per sample aligned HiFi reads, PCR duplicates marked, reads tagged by haplotype (HP tag) fastq demultiplexed HiFi reads for each sample ref GRCh38 reference used to generate BAM files TwistAllianceLongReadPGx_GeneList.txt gene list