There are two major scenarios for samples with no supplied gender:
1) Supplied data is missing for a few samples. In this case the samples should fail. This is the current situation.
2) Data is not available for any sample in the project. In this case we may wish for the samples to pass QC. We could provide an option to automatically pass the gender check for samples with missing supplied gender, instead of automatically failing.
There are two major scenarios for samples with no supplied gender: 1) Supplied data is missing for a few samples. In this case the samples should fail. This is the current situation. 2) Data is not available for any sample in the project. In this case we may wish for the samples to pass QC. We could provide an option to automatically pass the gender check for samples with missing supplied gender, instead of automatically failing.
See discussion in RT#457945.