Proper way to plot VCF files from structural variant callers
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6.4 years ago
Luca Beltrame ▴ 240

Hello,

I already made and annotated a number of VCF files with LUMPY and manta, and I'd like to find a way to properly view them: while I'm fine looking through them programmatically, it is useless for the biologists that will need to look at the data. Unfortunately, extensive Google searches haven't found many information. In particular, there aren't any standardized way to extract these information from VCF files for plotting, and tools like circos, while producing nice results, are hardly automatable and need a lot of trial and error to set things up.

All of this to say that I'd like to know if there are (relatively easy - format conversion is always possible) ways to visualize the output of SV callers such as those I mentioned, or at least with "reduced effort" with regards to input. I have tried intansv from Bioconductor, but it can't parse LUMPY's VCF files (in fact, the exact file type required is not quite documented).

I understand this question has been asked before, but the software presented there isn't quite satisfactory (savant looks unmaintained and has severe issues with installation, IGV isn't too useful in this regard).

sequencing visualization circos • 2.8k views
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