Question: Script: VCF to 3 base mutation pattern
0
gravatar for Shicheng Guo
11 months ago by
Shicheng Guo8.2k
Shicheng Guo8.2k wrote:

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.

enter image description here

Thanks.

vcf • 263 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by Shicheng Guo8.2k
1

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

ADD REPLYlink written 11 months ago by zx87549.2k

What about indel data? Discard?

ADD REPLYlink written 11 months ago by MatthewP620

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

ADD REPLYlink written 11 months ago by Shicheng Guo8.2k

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?

ADD REPLYlink written 11 months ago by RamRS27k
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