search

weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
188 stars 73 forks source link

How is missing data handled in SAIGE-GENE? #311

Closed garyzhubc closed 2 years ago

garyzhubc commented 3 years ago

How is missing data handled in SAIGE-GENE?

weizhouUMICH commented 3 years ago

Here is the option to specify the way to handle missing dosages/genotypes.

https://github.com/weizhouUMICH/SAIGE/blob/master/extdata/step2_SPAtests.R#L45

weizhouUMICH commented 2 years ago

We have just released a new version 1.0.0. It has substantial computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests and clearer log output. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/ The program will be maintained by multiple SAIGE developers there. The docker image has been updated. Please feel free to try the version 1.0.0 and report issues if any.

Thanks! Wei