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weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
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Is it possible to perform only genotype Quality Control with SAIGE? #379

Closed raimondsre closed 2 years ago

raimondsre commented 2 years ago

I would like to perform genotype quality control with SAIGE software as in https://www.nature.com/articles/s41586-021-03767-x

weizhouUMICH commented 2 years ago

yes, you may used --minMAF 0.01 and --minInfo=0.6 in step 2