Tool/method to calculate the sequence context of variants?
Before I go trying to reinvent the wheel I am wondering if anyone knows of a handy tool to answer the following.
I am trying to replicate a figure the shows the sequence context of specific variants (e.g. C to A SNVs). So for all C to A variants the figure shows the frequency of event where the variant lies between AA, AC, AG, AT, CA, CC, CG, CT, etc.
This relates to figure 3 of 'doi.org/10.1038/s41598-020-61807-4' if you have access.
The long way round is to extract the three base sequence for every variant, but is there a tool that generates this type of information?
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