add_metadata            add_metadata
af_distribution         af_distribution
arrange_data            arrange_data
dNdS_segment            dNdS_segment
example_filtered_SNV_df
                        Example Dataframe The DF_filt_SNVs dataframe
                        created in the vignette
filter_variants         filter_variants
merge_replicates        merge_replicates
plot_shannon            plot_shannon
position_allele_freq    position_allele_freq
prepare_annotations     prepare_annotations
read_reference_fasta_dna
                        read_reference_fasta_dna
shannon_entropy         shannon_entropy
shared_snv_plot         shared_snv_plot
shared_snv_table        shared_snv_table
snpeff_info             snpeff_info
snv_genome              snv_genome
snv_location            snv_location
snv_segment             snv_segment
tally_it                tally_it
tstv_plot               tstv_plot
tstv_ratio              tstv_ratio
