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
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williamsbrian5064
use bctools view with option --samples-file or --samples to keep/remove the sample of each group.
Extract the AF field with bcftools query
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?
I'm not sure bcf tools can do that?
bcftools query
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
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Sorry about that. I thought I did that
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Good description of data. Could you please post example data and expected output? @op
Maybe use vcfR R package?