Software to calculate frequency of mutation by group

Question

[williamsbrian5064]

Hi,

I have a vcf file with 3 unique groups. Each group has 10 samples, we'll call them group A, group B, and control group. I want to calculate the frequency a mutation appears in group A and group B. I am just trying to figure out what's the best software to use to do this? I know there are programs like VEP and snpEff but I am not sure they can do this? I could be wrong though. I used snpEff already to get variant locations but haven't been able to figure this out. It would be nice if snpEff or VEP could do this but I can also use R to combine my fines if I need to. Ideally I'd like to be able to do something like frequency group A >= 0, frequency group B >=0, and frequency control ==0

Any help would be amazing! Thanks in advance

[cpad0112]

Good description of data. Could you please post example data and expected output? @op

[zx8754]

Maybe use vcfR R package?

Answer 1

[Pierre Lindenbaum]

use bctools view with option --samples-file or --samples to keep/remove the sample of each group. Extract the AF field with bcftools query

[williamsbrian5064]

I really just want like a .txt file like snpEff or VEP generates. Something that I can visualize. I'm not sure bcf tools can do that?

[Pierre Lindenbaum]

I'm not sure bcf tools can do that?

bcftools query

[williamsbrian5064]

I had to do a bit more reading. They don't make it super clear about the output format. Ended up working for me! As always, thanks for the help Pierre

[Pierre Lindenbaum]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[williamsbrian5064]

Sorry about that. I thought I did that