Hello, I want to generate stats of various types of statistical information from reference population in gnomAD/ExAC reference population and wanted to know what might be the best way to accomplish this.
Could not find any open-source tool/ script online and in some online code repos.
Any help in this direction would be most appreciated.
1 answer
The easiest way I see is to download the raw data in VCF (variant calling files) format (Sites VCF) and use some kind of tool that summarizes VCF files. (Example, haven't tried it.)
To do anything serious, most likely you would have to use some programming/scripting language. R is great for that, python works too.
Make sure you understand what goes into ExAC/gnomAD too. Whatever hypothesis you have about what you find in ExAC should consider what kind of exomes are included, what the coverage is per site, stats reported by ExAC such as the per gene pLI (percentile of loss-of-function intolerance) and misense count z-scores.
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I'm sorry, what?
Have you tried R?