Performs variant calling on SARS-CoV-2 in waster water samples and identifies mutations in the Spike gene associated with known VOCs and VUIs on the Google Cloud Terra Platform.
Takes as input an Array[File] of coordinate sorted bams from the following workflows: illumina-preprocessing-assembly (for paired-end illumina data), nanopore-preprocessing-assembly (for nanopore data), and COVIDSeqSEassembly (for single-end sequencing using th

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