Question: Script: VCF to 3 base mutation pattern
0
gravatar for Shicheng Guo
6 days ago by
Shicheng Guo7.5k
Shicheng Guo7.5k 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 • 90 views
ADD COMMENTlink modified 6 days ago • written 6 days ago by Shicheng Guo7.5k
1

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

ADD REPLYlink written 6 days ago by zx87547.5k

What about indel data? Discard?

ADD REPLYlink written 6 days ago by MatthewP110

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

ADD REPLYlink written 6 days ago by Shicheng Guo7.5k

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 6 days ago by RamRS22k
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