Converting a mutation data file into vcf?

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6.9 years ago

prathyushakonda ▴ 20

Hello, I have a dataset of mutations which consists of information about gene, CDS mutation, sample and AA mutation. I was wondering if there are tools to annotate this kind of data? Is it possible to convert this to vcf at all? or is there an easier way to generate consensus sequences based on this data?

This is how the file looks like

Gene_Name   Sample_Name CDS_Mutation AA_Mutation
39340   05-165O c.71C>T p.T24I
A1BG    06-134H1    c.330G>A    p.L110L
A1BG    TCGA-CH-5752-01 c.480G>A    p.E160E
A1BG    TCGA-EJ-5499-01 c.733C>T    p.R245C

next-gen-sequencing exome • 1.7k views

ADD COMMENT • link updated 11 months ago by Ram 43k • written 6.9 years ago by prathyushakonda ▴ 20

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It would be definitely helpful if you show us how this file looks like.

ADD REPLY • link 6.9 years ago by WouterDeCoster 47k

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Sorry about that. This is how it looks.

Gene_Name   Sample_Name CDS_Mutation     AA_Mutation
39340   05-165O c.71C>T p.T24I
A1BG    06-134H1    c.330G>A    p.L110L
A1BG    TCGA-CH-5752-01 c.480G>A    p.E160E
A1BG    TCGA-EJ-5499-01 c.733C>T    p.R245C
A1CF    DU-145  c.688G>T    p.V230L

ADD REPLY • link updated 6.9 years ago by WouterDeCoster 47k • written 6.9 years ago by prathyushakonda ▴ 20

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I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

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ADD REPLY • link 6.9 years ago by WouterDeCoster 47k

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