Extracting mutation and Mutation spectrum
Is there any tools or packages which can help me extract mutation information and essentially plot them to know the occurrence frequency of mutation or visualize the mutation spectra?
I have 1) Merged vcf file for all my sample information , 2) A jsonl tree information with annotated mutations and 3) a Mutation annotated (MAT) proto buffer file.
Which of these files are commonly used to generate mutation information and possibly visualize the mutation spectrum? Thank you
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