Script: VCF to 3 base mutation pattern

Question

[Shicheng Guo]

Hi All,

Who can share a script to transfer mutation VCF files to 3-base mutation pattern:

Bekow is the output i want to obtain. I want the counts for each mutation category.

Thanks.

[zx8754]

Provide example input, expected output, and what have you tried so far.

[MatthewP]

What about indel data? Discard?

[Shicheng Guo]

Yes，discard indel and complex mutation type. another problem maybe for one mutation, it may have 2 annation.

[Ram]

What are the numbers that are attached to each change? These 3-base changes - are they codon changes or just +/- 1 nucleotide? Are you looking for changes in the reference strand only or is this strand specific?

More importantly, why are you doing this exercise? What do you hope to accomplish from it?