Before you begin | Compute a phylogenetic tree | Identify clones and assign cells to clones | Parameter choice | Session information

Overview | Introduction | Package goals | Genome availability | Input data | Counting nucleotides from BAM files | Counting function examples and explanations | Calling and filtering variants | Calling mutations based on an exclusionlist | Calling mutations based on variants shared within a cohort | Example of Exclusionlist filtering | Example of Cohort filtering | Session information