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dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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The model underlying GLnexus calling #258

Open Axze-rgb opened 3 years ago

Axze-rgb commented 3 years ago

Hello,

is it possible to have some infos on the underlying model which decides to keep or reject a variant? If I understood well it's a Bayesian model, right? I would be interested to see the formula and its priors. It's pure curiosity.

Thanks a lot

mlin commented 3 years ago

The keep/filter decision is simpler, described in the Configuration docs (see min_AQ1 and min_AQ2, and a few of the other misc settings)

Given a called variant, the logic to revise the called zygosity (0/1 or 1/1) and GQ is a little bit more involved, but shouldn't be too hard to follow in the code

HTH