R Package for Visualizing SNVs from "sites only" VCF (population variants)
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13 months ago
j.lunger18 ▴ 30

I found GenVisR, which has a nice variant visualization tool (Lollipop), but the VCF I have is downloaded from gnomAD, so does not have individual sample information. Is there another tool that can be used to visualize this kind of data?

R SNVs VCF • 531 views
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If your VCF does not sample information, then how will any tool be able to use that information?

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Population "sites only" VCFs can still be annotated, so I have a lot of information on predicted impact of each variant on protein function, frequency in different populations, etc. I have a lot of information on each variant, but no sample-specific information.

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Considering this type of file is what gnomAD variants are formatted in, I figured there may be tools to visualize annotated versions of these files.

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So do you want to add annotations to the VCF?

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I already annotated the files. I want a tool that can take all that information associated with each variant and visualize it in a way that is more digestible than a huge dataframe aka a mutation lollipop chart, multiplexed graphs, etc.

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Ideally something that can load in ensembl transcript and protein domain information for a gene of interest

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But didn't you say you already found GenVisR?

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