Variant analysis
Variants were called using LoFreq (version 2.1.1), FreeBayes (version 0.9.9) and proprietary methods. VariantPlex pipeline parameters were adjusted to accommodate the large footprint of SNiPDx and minimize background noise within variant calls. Variant calls <300 base pairs from the nearest gene-specific primers within regions of interest in reads with a minimum base quality of 22, and with a minimum allele fraction of 0.02, were reported. Genes, transcripts and consequences of variants were accessed through Alamut Batch (Interactive BioSoftware) using database version 1.5-2020.11.25. A variant call format file for each sample was generated using VCFtools version 0.1.11.