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?
If your VCF does not sample information, then how will any tool be able to use that information?
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.
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.
So do you want to add annotations to the VCF?
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.
Ideally something that can load in ensembl transcript and protein domain information for a gene of interest
But didn't you say you already found GenVisR?
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