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Script: VCF to 3 base mutation pattern

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.

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Thanks.

vcf
• 1,615 views • link
written by Shicheng Guo Shicheng Guo

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

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written by zx8754 zx8754

What about indel data? Discard?

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written by MatthewP MatthewP

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

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written by Shicheng Guo Shicheng Guo

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?

• 0 views • link
written by Ram Ram

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