Package: vivaldi 1.0.1

Load the Vivaldi package | Vignette data set | Step 1: Set path for variant data and metadata | Step 2: Loading data and arranging | Load VCF files into a dataframe | Merging Replicate Sequence Data | Compare the allele frequencies between replicate 1 and 2 | Compare the similarity between the average allele frequency and the weighted average allele frequency | Filter out variants based on coverage and/or frequency cutoffs | Format SNPeff information | Remove duplicate variants in NS and MP | Add metadata | Step 3: Calculations and Visualization | Plot distribution of all minor variant frequencies | Count number of SNVs | Plot location of SNVs across segments | Plot number of SNVs per sample and per segment | Calculate Transition/Transversion Ratio | Plot TsTv | Calculate Shannon entropy | Plot shannon entropy per sample and per segment | Calculate dNdS ratio and plot per sample per protein product | Identify variants shared among samples | Print dataframe of variants shared among samples for further analysis | Isolate variant of interest and plot AF at that position in all samples