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weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
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minInfo and negative INFO scores #308

Closed frahimov closed 2 years ago

frahimov commented 3 years ago

Hello. The X chromosome summary statistics file contains lots of negative imputationInfo scores, even though I applied --minInfo=0.8. Is this normal? And what causes this?

weizhouUMICH commented 2 years ago

Sorry fo the late reply! 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