Question: Interpreting stats from gnomAD/ ExAC reference population
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gravatar for win
24 months ago by
win840
India
win840 wrote:

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.

exac • 1.3k views
ADD COMMENTlink modified 13 days ago by Biostar ♦♦ 20 • written 24 months ago by win840
2

stats of various type of statistical information

I'm sorry, what?

Could not find any open-source tool/ script online

Have you tried R?

ADD REPLYlink written 24 months ago by RamRS28k
0
gravatar for manuel.belmadani
24 months ago by
Canada
manuel.belmadani1.2k wrote:

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.

ADD COMMENTlink written 24 months ago by manuel.belmadani1.2k
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