For visualizing motif structure and methylation levels of TR alleles, use VisuaMiTRa, an auxiliary visualization tool that runs in a web browser and accepts ATaRVa VCF files as input.
To include motif decomposition and methylation information in the VCF, run ATaRVa with the --decompose and --methviz flags. Motif decomposition can still be generated from the default VCF even if --decompose is not specified; however, the --methviz flag is required for visualizing methylation levels.
VisuaMiTRa allows users to compare motif structure and methylation levels within the same allele in single-sample mode and also supports multi-sample analysis.
Overview of visuamitra